problem with function
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@iain-gallagher-2532
Last seen 8.7 years ago
United Kingdom
Hello List I wonder if someone would help me with the following function. cumulMetric <- function(deMirPresGenes, deMirs){ #need to match position of each miR in deMirPresGenes with its FC to form a vector of FC in correct order fc <- deMirs fcVector <- as.numeric(with (fc, FC[match(deMirPresGenes1[,4], Probe)] ) ) #multiply fc by context score for each interaction metric <- fcVector * as.numeric(deMirPresGenes[,11]) geneMetric <- cbind(deMirPresGenes[,2], as.numeric(metric)) #make cumul weighted score listMetric <- unstack(geneMetric, as.numeric(geneMetric[,2])~geneMetric[,1]) listMetric <- as.data.frame(sapply(listMetric,sum)) #returns a dataframe colnames(listMetric) <- c('cumulMetric') #return whole list return(listMetric) } deMirPresGenes looks like this: Gene.ID Gene.Symbol Species.ID miRNA Site.type UTR_start UTR_end X3pairing_contr local_AU_contr position_contr context_score context_percentile 22848 AAK1 9606 hsa-miR-183 2 1546 1552 -0.026 -0.047 0.099 -0.135 47 19 ABCA1 9606 hsa-miR-183 2 1366 1372 -0.011 -0.048 0.087 -0.133 46 20 ABCA2 9606 hsa-miR-495 2 666 672 -0.042 -0.092 -0.035 -0.33 93 23456 ABCB10 9606 hsa-miR-183 3 1475 1481 0.003 -0.109 -0.05 -0.466 98 6059 ABCE1 9606 hsa-miR-495 2 1474 1480 0.005 -0.046 0.006 -0.196 58 55324 ABCF3 9606 hsa-miR-1275 3 90 96 0.007 0.042 -0.055 -0.316 94 The aim of the function is to extract a dataframe of gene symbols along with a weighted score from the above data. The weighted score is the FC column of deMirs * the context_score column of deMirPresGenes. This is easy peasy! Where I'm falling down is that if I run this function it complains that 'geneMetric' can't be found. Hmm - I've run it all line by line (i.e. not as a function) and it works but wrapped up like this it fails! e.g. >testF2 <- cumulMetric(testF1, deMirs$up) Error in eval(expr, envir, enclos) : object 'geneMetric' not found deMirs$up looks like this: Probe FC hsa-miR-183 2.63 hsa-miR-1275 2.74 hsa-miR-495 3.13 hsa-miR-886-3p 3.73 hsa-miR-886-5p 3.97 hsa-miR-144* 6.62 hsa-miR-451 7.94 Could someone possibly point out where I falling down. Thanks i > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.12.0 >
miRNA miRNA • 1.7k views
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cstrato ★ 3.9k
@cstrato-908
Last seen 5.5 years ago
Austria
I am not sure but I would say that deMirPresGenes1 does not exist. Regards Christian On 12/17/10 6:42 PM, Iain Gallagher wrote: > Hello List > > I wonder if someone would help me with the following function. > > cumulMetric<- function(deMirPresGenes, deMirs){ > > #need to match position of each miR in deMirPresGenes with its FC to form a vector of FC in correct order > fc<- deMirs > fcVector<- as.numeric(with (fc, FC[match(deMirPresGenes1[,4], Probe)] ) ) > > #multiply fc by context score for each interaction > metric<- fcVector * as.numeric(deMirPresGenes[,11]) > geneMetric<- cbind(deMirPresGenes[,2], as.numeric(metric)) > > #make cumul weighted score > listMetric<- unstack(geneMetric, as.numeric(geneMetric[,2])~geneMetric[,1]) > listMetric<- as.data.frame(sapply(listMetric,sum)) #returns a dataframe > colnames(listMetric)<- c('cumulMetric') > > #return whole list > return(listMetric) > } > > deMirPresGenes looks like this: > > Gene.ID Gene.Symbol Species.ID miRNA Site.type UTR_start UTR_end X3pairing_contr local_AU_contr position_contr context_score context_percentile > 22848 AAK1 9606 hsa-miR-183 2 1546 1552 -0.026 -0.047 0.099 -0.135 47 > 19 ABCA1 9606 hsa-miR-183 2 1366 1372 -0.011 -0.048 0.087 -0.133 46 > 20 ABCA2 9606 hsa-miR-495 2 666 672 -0.042 -0.092 -0.035 -0.33 93 > 23456 ABCB10 9606 hsa-miR-183 3 1475 1481 0.003 -0.109 -0.05 -0.466 98 > 6059 ABCE1 9606 hsa-miR-495 2 1474 1480 0.005 -0.046 0.006 -0.196 58 > 55324 ABCF3 9606 hsa-miR-1275 3 90 96 0.007 0.042 -0.055 -0.316 94 > > > The aim of the function is to extract a dataframe of gene symbols along with a weighted score from the above data. The weighted score is the FC column of deMirs * the context_score column of deMirPresGenes. This is easy peasy! > > Where I'm falling down is that if I run this function it complains that 'geneMetric' can't be found. Hmm - I've run it all line by line (i.e. not as a function) and it works but wrapped up like this it fails! > > e.g. > >> testF2<- cumulMetric(testF1, deMirs$up) > Error in eval(expr, envir, enclos) : object 'geneMetric' not found > > deMirs$up looks like this: > > Probe FC > hsa-miR-183 2.63 > hsa-miR-1275 2.74 > hsa-miR-495 3.13 > hsa-miR-886-3p 3.73 > hsa-miR-886-5p 3.97 > hsa-miR-144* 6.62 > hsa-miR-451 7.94 > > Could someone possibly point out where I falling down. > > Thanks > > i > >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C > [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 > [7] LC_PAPER=en_GB.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.12.0 >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Sorry. That was a typo. In my script deMirPresGenes1[,4] is deMirPresGenes[,4]. Just to be sure I'm going about this the right way though I should say that at the moment I assign the output of another function to a variable called 'tf1' - this object is the same as the deMirPresGenes is my previous email. This is then fed to my problem function using positional matching. e.g. tf2 <- cumulMetric(tf1, deMirs) Which leads to: Error in eval(expr, envir, enclos) : object 'geneMetric' not found Hey ho! i --- On Fri, 17/12/10, cstrato <cstrato at="" aon.at=""> wrote: > From: cstrato <cstrato at="" aon.at=""> > Subject: Re: [BioC] problem with function > To: "Iain Gallagher" <iaingallagher at="" btopenworld.com=""> > Cc: "bioconductor" <bioconductor at="" stat.math.ethz.ch=""> > Date: Friday, 17 December, 2010, 18:40 > I am not sure but I would say that > deMirPresGenes1 does not exist. > > Regards > Christian > > > On 12/17/10 6:42 PM, Iain Gallagher wrote: > > Hello List > > > > I wonder if someone would help me with the following > function. > > > > cumulMetric<- function(deMirPresGenes, deMirs){ > > ??? > > #need to match position of each miR in deMirPresGenes > with its FC to form a vector of FC in correct order > > ??? fc<- deMirs > > ??? fcVector<- as.numeric(with (fc, > FC[match(deMirPresGenes1[,4], Probe)] ) ) > > > > ??? #multiply fc by context score for > each interaction > > ??? metric<- fcVector * > as.numeric(deMirPresGenes[,11]) > > ??? geneMetric<- > cbind(deMirPresGenes[,2], as.numeric(metric)) > > > >?????? #make cumul > weighted score > > ??? listMetric<- unstack(geneMetric, > as.numeric(geneMetric[,2])~geneMetric[,1]) > > ??? listMetric<- > as.data.frame(sapply(listMetric,sum)) #returns a dataframe > > ??? colnames(listMetric)<- > c('cumulMetric') > > > > ??? #return whole list > > ??? return(listMetric) > > } > > > > deMirPresGenes looks like this: > > > > Gene.ID??? > Gene.Symbol??? Species.ID??? > miRNA??? Site.type??? > UTR_start??? UTR_end??? > X3pairing_contr??? > local_AU_contr??? > position_contr??? > context_score??? context_percentile > > 22848??? AAK1??? > 9606??? hsa-miR-183??? > 2??? 1546??? > 1552??? -0.026??? > -0.047??? 0.099??? > -0.135??? 47 > > 19??? ABCA1??? > 9606??? hsa-miR-183??? > 2??? 1366??? > 1372??? -0.011??? > -0.048??? 0.087??? > -0.133??? 46 > > 20??? ABCA2??? > 9606??? hsa-miR-495??? > 2??? 666??? > 672??? -0.042??? > -0.092??? -0.035??? > -0.33??? 93 > > 23456??? ABCB10??? > 9606??? hsa-miR-183??? > 3??? 1475??? > 1481??? 0.003??? > -0.109??? -0.05??? > -0.466??? 98 > > 6059??? ABCE1??? > 9606??? hsa-miR-495??? > 2??? 1474??? > 1480??? 0.005??? > -0.046??? 0.006??? > -0.196??? 58 > > 55324??? ABCF3??? > 9606??? hsa-miR-1275??? > 3??? 90??? > 96??? 0.007??? > 0.042??? -0.055??? > -0.316??? 94 > > > > > > The aim of the function is to extract a dataframe of > gene symbols along with a weighted score from the above > data. The weighted score is the FC column of deMirs * the > context_score column of deMirPresGenes. This is easy peasy! > > > > Where I'm falling down is that if I run this function > it complains that 'geneMetric' can't be found. Hmm - I've > run it all line by line (i.e. not as a function) and it > works but wrapped up like this it fails! > > > > e.g. > > > >> testF2<- cumulMetric(testF1, deMirs$up) > > Error in eval(expr, envir, enclos) : object > 'geneMetric' not found > > > > deMirs$up looks like this: > > > > Probe??? FC > > hsa-miR-183??? 2.63 > > hsa-miR-1275??? 2.74 > > hsa-miR-495??? 3.13 > > hsa-miR-886-3p??? 3.73 > > hsa-miR-886-5p??? 3.97 > > hsa-miR-144*??? 6.62 > > hsa-miR-451??? 7.94 > > > > Could someone possibly point out where I falling > down. > > > > Thanks > > > > i > > > >> sessionInfo() > > R version 2.12.0 (2010-10-15) > > Platform: x86_64-pc-linux-gnu (64-bit) > > > > locale: > >???[1] LC_CTYPE=en_GB.utf8? ? > ???LC_NUMERIC=C > >???[3] LC_TIME=en_GB.utf8? ? > ? ? LC_COLLATE=en_GB.utf8 > >???[5] LC_MONETARY=C? ? ? > ? ? ???LC_MESSAGES=en_GB.utf8 > >???[7] LC_PAPER=en_GB.utf8? ? > ???LC_NAME=C > >???[9] LC_ADDRESS=C? ? ? > ? ? ? ? LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats? ???graphics? > grDevices utils? ???datasets? > methods???base > > > > loaded via a namespace (and not attached): > > [1] tools_2.12.0 > >> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >
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What is FC[]? It is not passed to the function. Christan On 12/17/10 8:11 PM, Iain Gallagher wrote: > Sorry. > > That was a typo. In my script deMirPresGenes1[,4] is deMirPresGenes[,4]. > > Just to be sure I'm going about this the right way though I should say that at the moment I assign the output of another function to a variable called 'tf1' - this object is the same as the deMirPresGenes is my previous email. > > This is then fed to my problem function using positional matching. > > e.g. tf2<- cumulMetric(tf1, deMirs) > > Which leads to: > > Error in eval(expr, envir, enclos) : object 'geneMetric' not found > > Hey ho! > > i > > --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at=""> wrote: > >> From: cstrato<cstrato at="" aon.at=""> >> Subject: Re: [BioC] problem with function >> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> >> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> >> Date: Friday, 17 December, 2010, 18:40 >> I am not sure but I would say that >> deMirPresGenes1 does not exist. >> >> Regards >> Christian >> >> >> On 12/17/10 6:42 PM, Iain Gallagher wrote: >>> Hello List >>> >>> I wonder if someone would help me with the following >> function. >>> >>> cumulMetric<- function(deMirPresGenes, deMirs){ >>> >>> #need to match position of each miR in deMirPresGenes >> with its FC to form a vector of FC in correct order >>> fc<- deMirs >>> fcVector<- as.numeric(with (fc, >> FC[match(deMirPresGenes1[,4], Probe)] ) ) >>> >>> #multiply fc by context score for >> each interaction >>> metric<- fcVector * >> as.numeric(deMirPresGenes[,11]) >>> geneMetric<- >> cbind(deMirPresGenes[,2], as.numeric(metric)) >>> >>> #make cumul >> weighted score >>> listMetric<- unstack(geneMetric, >> as.numeric(geneMetric[,2])~geneMetric[,1]) >>> listMetric<- >> as.data.frame(sapply(listMetric,sum)) #returns a dataframe >>> colnames(listMetric)<- >> c('cumulMetric') >>> >>> #return whole list >>> return(listMetric) >>> } >>> >>> deMirPresGenes looks like this: >>> >>> Gene.ID >> Gene.Symbol Species.ID >> miRNA Site.type >> UTR_start UTR_end >> X3pairing_contr >> local_AU_contr >> position_contr >> context_score context_percentile >>> 22848 AAK1 >> 9606 hsa-miR-183 >> 2 1546 >> 1552 -0.026 >> -0.047 0.099 >> -0.135 47 >>> 19 ABCA1 >> 9606 hsa-miR-183 >> 2 1366 >> 1372 -0.011 >> -0.048 0.087 >> -0.133 46 >>> 20 ABCA2 >> 9606 hsa-miR-495 >> 2 666 >> 672 -0.042 >> -0.092 -0.035 >> -0.33 93 >>> 23456 ABCB10 >> 9606 hsa-miR-183 >> 3 1475 >> 1481 0.003 >> -0.109 -0.05 >> -0.466 98 >>> 6059 ABCE1 >> 9606 hsa-miR-495 >> 2 1474 >> 1480 0.005 >> -0.046 0.006 >> -0.196 58 >>> 55324 ABCF3 >> 9606 hsa-miR-1275 >> 3 90 >> 96 0.007 >> 0.042 -0.055 >> -0.316 94 >>> >>> >>> The aim of the function is to extract a dataframe of >> gene symbols along with a weighted score from the above >> data. The weighted score is the FC column of deMirs * the >> context_score column of deMirPresGenes. This is easy peasy! >>> >>> Where I'm falling down is that if I run this function >> it complains that 'geneMetric' can't be found. Hmm - I've >> run it all line by line (i.e. not as a function) and it >> works but wrapped up like this it fails! >>> >>> e.g. >>> >>>> testF2<- cumulMetric(testF1, deMirs$up) >>> Error in eval(expr, envir, enclos) : object >> 'geneMetric' not found >>> >>> deMirs$up looks like this: >>> >>> Probe FC >>> hsa-miR-183 2.63 >>> hsa-miR-1275 2.74 >>> hsa-miR-495 3.13 >>> hsa-miR-886-3p 3.73 >>> hsa-miR-886-5p 3.97 >>> hsa-miR-144* 6.62 >>> hsa-miR-451 7.94 >>> >>> Could someone possibly point out where I falling >> down. >>> >>> Thanks >>> >>> i >>> >>>> sessionInfo() >>> R version 2.12.0 (2010-10-15) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_GB.utf8 >> LC_NUMERIC=C >>> [3] LC_TIME=en_GB.utf8 >> LC_COLLATE=en_GB.utf8 >>> [5] LC_MONETARY=C >> LC_MESSAGES=en_GB.utf8 >>> [7] LC_PAPER=en_GB.utf8 >> LC_NAME=C >>> [9] LC_ADDRESS=C >> LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics >> grDevices utils datasets >> methods base >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.12.0 >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi FC is the second column of the deMirs variable. deMirs is a dataframe with 2 columns - Probe (e.g. hsa-miR-145) and FC (e.g 1.45). Using 'with' allows me to use deMirs as an 'environment'. I thus don't have to pass FC explicitly. Cheers i --- On Fri, 17/12/10, cstrato <cstrato at="" aon.at=""> wrote: > From: cstrato <cstrato at="" aon.at=""> > Subject: Re: [BioC] problem with function > To: "Iain Gallagher" <iaingallagher at="" btopenworld.com=""> > Cc: "bioconductor" <bioconductor at="" stat.math.ethz.ch=""> > Date: Friday, 17 December, 2010, 20:39 > What is FC[]?? It is not passed > to the function. Christan > > On 12/17/10 8:11 PM, Iain Gallagher wrote: > > Sorry. > > > > That was a typo. In my script deMirPresGenes1[,4] is > deMirPresGenes[,4]. > > > > Just to be sure I'm going about this the right way > though I should say that at the moment I assign the output > of another function to a variable called 'tf1' - this object > is the same as the deMirPresGenes is my previous email. > > > > This is then fed to my problem function using > positional matching. > > > > e.g. tf2<- cumulMetric(tf1, deMirs) > > > > Which leads to: > > > > Error in eval(expr, envir, enclos) : object > 'geneMetric' not found > > > > Hey ho! > > > > i > > > > --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at="">? > wrote: > > > >> From: cstrato<cstrato at="" aon.at=""> > >> Subject: Re: [BioC] problem with function > >> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> > >> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> > >> Date: Friday, 17 December, 2010, 18:40 > >> I am not sure but I would say that > >> deMirPresGenes1 does not exist. > >> > >> Regards > >> Christian > >> > >> > >> On 12/17/10 6:42 PM, Iain Gallagher wrote: > >>> Hello List > >>> > >>> I wonder if someone would help me with the > following > >> function. > >>> > >>> cumulMetric<- function(deMirPresGenes, > deMirs){ > >>> > >>> #need to match position of each miR in > deMirPresGenes > >> with its FC to form a vector of FC in correct > order > >>>? ? ? fc<- deMirs > >>>? ? ? fcVector<- > as.numeric(with (fc, > >> FC[match(deMirPresGenes1[,4], Probe)] ) ) > >>> > >>>? ? ? #multiply fc by context > score for > >> each interaction > >>>? ? ? metric<- fcVector * > >> as.numeric(deMirPresGenes[,11]) > >>>? ? ? geneMetric<- > >> cbind(deMirPresGenes[,2], as.numeric(metric)) > >>> > >>>? ? ? ???#make > cumul > >> weighted score > >>>? ? ? listMetric<- > unstack(geneMetric, > >> as.numeric(geneMetric[,2])~geneMetric[,1]) > >>>? ? ? listMetric<- > >> as.data.frame(sapply(listMetric,sum)) #returns a > dataframe > >>>? ? ? colnames(listMetric)<- > >> c('cumulMetric') > >>> > >>>? ? ? #return whole list > >>>? ? ? return(listMetric) > >>> } > >>> > >>> deMirPresGenes looks like this: > >>> > >>> Gene.ID > >> Gene.Symbol? ? Species.ID > >> miRNA? ? Site.type > >> UTR_start? ? UTR_end > >> X3pairing_contr > >> local_AU_contr > >> position_contr > >> context_score? ? context_percentile > >>> 22848? ? AAK1 > >> 9606? ? hsa-miR-183 > >> 2? ? 1546 > >> 1552? ? -0.026 > >> -0.047? ? 0.099 > >> -0.135? ? 47 > >>> 19? ? ABCA1 > >> 9606? ? hsa-miR-183 > >> 2? ? 1366 > >> 1372? ? -0.011 > >> -0.048? ? 0.087 > >> -0.133? ? 46 > >>> 20? ? ABCA2 > >> 9606? ? hsa-miR-495 > >> 2? ? 666 > >> 672? ? -0.042 > >> -0.092? ? -0.035 > >> -0.33? ? 93 > >>> 23456? ? ABCB10 > >> 9606? ? hsa-miR-183 > >> 3? ? 1475 > >> 1481? ? 0.003 > >> -0.109? ? -0.05 > >> -0.466? ? 98 > >>> 6059? ? ABCE1 > >> 9606? ? hsa-miR-495 > >> 2? ? 1474 > >> 1480? ? 0.005 > >> -0.046? ? 0.006 > >> -0.196? ? 58 > >>> 55324? ? ABCF3 > >> 9606? ? hsa-miR-1275 > >> 3? ? 90 > >> 96? ? 0.007 > >> 0.042? ? -0.055 > >> -0.316? ? 94 > >>> > >>> > >>> The aim of the function is to extract a > dataframe of > >> gene symbols along with a weighted score from the > above > >> data. The weighted score is the FC column of > deMirs * the > >> context_score column of deMirPresGenes. This is > easy peasy! > >>> > >>> Where I'm falling down is that if I run this > function > >> it complains that 'geneMetric' can't be found. Hmm > - I've > >> run it all line by line (i.e. not as a function) > and it > >> works but wrapped up like this it fails! > >>> > >>> e.g. > >>> > >>>> testF2<- cumulMetric(testF1, > deMirs$up) > >>> Error in eval(expr, envir, enclos) : object > >> 'geneMetric' not found > >>> > >>> deMirs$up looks like this: > >>> > >>> Probe? ? FC > >>> hsa-miR-183? ? 2.63 > >>> hsa-miR-1275? ? 2.74 > >>> hsa-miR-495? ? 3.13 > >>> hsa-miR-886-3p? ? 3.73 > >>> hsa-miR-886-5p? ? 3.97 > >>> hsa-miR-144*? ? 6.62 > >>> hsa-miR-451? ? 7.94 > >>> > >>> Could someone possibly point out where I > falling > >> down. > >>> > >>> Thanks > >>> > >>> i > >>> > >>>> sessionInfo() > >>> R version 2.12.0 (2010-10-15) > >>> Platform: x86_64-pc-linux-gnu (64-bit) > >>> > >>> locale: > >>>? ???[1] > LC_CTYPE=en_GB.utf8 > >>? ???LC_NUMERIC=C > >>>? ???[3] > LC_TIME=en_GB.utf8 > >>? ? ? LC_COLLATE=en_GB.utf8 > >>>? ???[5] LC_MONETARY=C > >>? ? ? > ???LC_MESSAGES=en_GB.utf8 > >>>? ???[7] > LC_PAPER=en_GB.utf8 > >>? ???LC_NAME=C > >>>? ???[9] LC_ADDRESS=C > >>? ? ? ? ? LC_TELEPHONE=C > >>> [11] LC_MEASUREMENT=en_GB.utf8 > LC_IDENTIFICATION=C > >>> > >>> attached base packages: > >>> [1] stats? ???graphics > >> grDevices utils? ???datasets > >> methods???base > >>> > >>> loaded via a namespace (and not attached): > >>> [1] tools_2.12.0 > >>>> > >>> > >>> > _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > >> > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >
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At the moment I have no idea, but what I would do in this case is to put print() statements after each line to see where it fails. Christian On 12/17/10 10:59 PM, Iain Gallagher wrote: > Hi > > FC is the second column of the deMirs variable. deMirs is a dataframe with 2 columns - Probe (e.g. hsa-miR-145) and FC (e.g 1.45). Using 'with' allows me to use deMirs as an 'environment'. I thus don't have to pass FC explicitly. > > Cheers > > i > > --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at=""> wrote: > >> From: cstrato<cstrato at="" aon.at=""> >> Subject: Re: [BioC] problem with function >> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> >> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> >> Date: Friday, 17 December, 2010, 20:39 >> What is FC[]? It is not passed >> to the function. Christan >> >> On 12/17/10 8:11 PM, Iain Gallagher wrote: >>> Sorry. >>> >>> That was a typo. In my script deMirPresGenes1[,4] is >> deMirPresGenes[,4]. >>> >>> Just to be sure I'm going about this the right way >> though I should say that at the moment I assign the output >> of another function to a variable called 'tf1' - this object >> is the same as the deMirPresGenes is my previous email. >>> >>> This is then fed to my problem function using >> positional matching. >>> >>> e.g. tf2<- cumulMetric(tf1, deMirs) >>> >>> Which leads to: >>> >>> Error in eval(expr, envir, enclos) : object >> 'geneMetric' not found >>> >>> Hey ho! >>> >>> i >>> >>> --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at=""> >> wrote: >>> >>>> From: cstrato<cstrato at="" aon.at=""> >>>> Subject: Re: [BioC] problem with function >>>> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> >>>> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> >>>> Date: Friday, 17 December, 2010, 18:40 >>>> I am not sure but I would say that >>>> deMirPresGenes1 does not exist. >>>> >>>> Regards >>>> Christian >>>> >>>> >>>> On 12/17/10 6:42 PM, Iain Gallagher wrote: >>>>> Hello List >>>>> >>>>> I wonder if someone would help me with the >> following >>>> function. >>>>> >>>>> cumulMetric<- function(deMirPresGenes, >> deMirs){ >>>>> >>>>> #need to match position of each miR in >> deMirPresGenes >>>> with its FC to form a vector of FC in correct >> order >>>>> fc<- deMirs >>>>> fcVector<- >> as.numeric(with (fc, >>>> FC[match(deMirPresGenes1[,4], Probe)] ) ) >>>>> >>>>> #multiply fc by context >> score for >>>> each interaction >>>>> metric<- fcVector * >>>> as.numeric(deMirPresGenes[,11]) >>>>> geneMetric<- >>>> cbind(deMirPresGenes[,2], as.numeric(metric)) >>>>> >>>>> #make >> cumul >>>> weighted score >>>>> listMetric<- >> unstack(geneMetric, >>>> as.numeric(geneMetric[,2])~geneMetric[,1]) >>>>> listMetric<- >>>> as.data.frame(sapply(listMetric,sum)) #returns a >> dataframe >>>>> colnames(listMetric)<- >>>> c('cumulMetric') >>>>> >>>>> #return whole list >>>>> return(listMetric) >>>>> } >>>>> >>>>> deMirPresGenes looks like this: >>>>> >>>>> Gene.ID >>>> Gene.Symbol Species.ID >>>> miRNA Site.type >>>> UTR_start UTR_end >>>> X3pairing_contr >>>> local_AU_contr >>>> position_contr >>>> context_score context_percentile >>>>> 22848 AAK1 >>>> 9606 hsa-miR-183 >>>> 2 1546 >>>> 1552 -0.026 >>>> -0.047 0.099 >>>> -0.135 47 >>>>> 19 ABCA1 >>>> 9606 hsa-miR-183 >>>> 2 1366 >>>> 1372 -0.011 >>>> -0.048 0.087 >>>> -0.133 46 >>>>> 20 ABCA2 >>>> 9606 hsa-miR-495 >>>> 2 666 >>>> 672 -0.042 >>>> -0.092 -0.035 >>>> -0.33 93 >>>>> 23456 ABCB10 >>>> 9606 hsa-miR-183 >>>> 3 1475 >>>> 1481 0.003 >>>> -0.109 -0.05 >>>> -0.466 98 >>>>> 6059 ABCE1 >>>> 9606 hsa-miR-495 >>>> 2 1474 >>>> 1480 0.005 >>>> -0.046 0.006 >>>> -0.196 58 >>>>> 55324 ABCF3 >>>> 9606 hsa-miR-1275 >>>> 3 90 >>>> 96 0.007 >>>> 0.042 -0.055 >>>> -0.316 94 >>>>> >>>>> >>>>> The aim of the function is to extract a >> dataframe of >>>> gene symbols along with a weighted score from the >> above >>>> data. The weighted score is the FC column of >> deMirs * the >>>> context_score column of deMirPresGenes. This is >> easy peasy! >>>>> >>>>> Where I'm falling down is that if I run this >> function >>>> it complains that 'geneMetric' can't be found. Hmm >> - I've >>>> run it all line by line (i.e. not as a function) >> and it >>>> works but wrapped up like this it fails! >>>>> >>>>> e.g. >>>>> >>>>>> testF2<- cumulMetric(testF1, >> deMirs$up) >>>>> Error in eval(expr, envir, enclos) : object >>>> 'geneMetric' not found >>>>> >>>>> deMirs$up looks like this: >>>>> >>>>> Probe FC >>>>> hsa-miR-183 2.63 >>>>> hsa-miR-1275 2.74 >>>>> hsa-miR-495 3.13 >>>>> hsa-miR-886-3p 3.73 >>>>> hsa-miR-886-5p 3.97 >>>>> hsa-miR-144* 6.62 >>>>> hsa-miR-451 7.94 >>>>> >>>>> Could someone possibly point out where I >> falling >>>> down. >>>>> >>>>> Thanks >>>>> >>>>> i >>>>> >>>>>> sessionInfo() >>>>> R version 2.12.0 (2010-10-15) >>>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> [1] >> LC_CTYPE=en_GB.utf8 >>>> LC_NUMERIC=C >>>>> [3] >> LC_TIME=en_GB.utf8 >>>> LC_COLLATE=en_GB.utf8 >>>>> [5] LC_MONETARY=C >>>> >> LC_MESSAGES=en_GB.utf8 >>>>> [7] >> LC_PAPER=en_GB.utf8 >>>> LC_NAME=C >>>>> [9] LC_ADDRESS=C >>>> LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_GB.utf8 >> LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics >>>> grDevices utils datasets >>>> methods base >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] tools_2.12.0 >>>>>> >>>>> >>>>> >> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >
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Thanks for the attention you've given this Christian. I'll do that and try and debug the output. Cheers Iain --- On Fri, 17/12/10, cstrato <cstrato at="" aon.at=""> wrote: > From: cstrato <cstrato at="" aon.at=""> > Subject: Re: [BioC] problem with function > To: "Iain Gallagher" <iaingallagher at="" btopenworld.com=""> > Cc: "bioconductor" <bioconductor at="" stat.math.ethz.ch=""> > Date: Friday, 17 December, 2010, 22:38 > At the moment I have no idea, but > what I would do in this case is to put > print() statements after each line to see where it fails. > > Christian > > On 12/17/10 10:59 PM, Iain Gallagher wrote: > > Hi > > > > FC is the second column of the deMirs variable. deMirs > is a dataframe with 2 columns - Probe (e.g. hsa-miR-145) and > FC (e.g 1.45). Using 'with' allows me to use deMirs as an > 'environment'. I thus don't have to pass FC explicitly. > > > > Cheers > > > > i > > > > --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at="">? > wrote: > > > >> From: cstrato<cstrato at="" aon.at=""> > >> Subject: Re: [BioC] problem with function > >> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> > >> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> > >> Date: Friday, 17 December, 2010, 20:39 > >> What is FC[]?? It is not passed > >> to the function. Christan > >> > >> On 12/17/10 8:11 PM, Iain Gallagher wrote: > >>> Sorry. > >>> > >>> That was a typo. In my script > deMirPresGenes1[,4] is > >> deMirPresGenes[,4]. > >>> > >>> Just to be sure I'm going about this the right > way > >> though I should say that at the moment I assign > the output > >> of another function to a variable called 'tf1' - > this object > >> is the same as the deMirPresGenes is my previous > email. > >>> > >>> This is then fed to my problem function using > >> positional matching. > >>> > >>> e.g. tf2<- cumulMetric(tf1, deMirs) > >>> > >>> Which leads to: > >>> > >>> Error in eval(expr, envir, enclos) : object > >> 'geneMetric' not found > >>> > >>> Hey ho! > >>> > >>> i > >>> > >>> --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at=""> > >> wrote: > >>> > >>>> From: cstrato<cstrato at="" aon.at=""> > >>>> Subject: Re: [BioC] problem with function > >>>> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> > >>>> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> > >>>> Date: Friday, 17 December, 2010, 18:40 > >>>> I am not sure but I would say that > >>>> deMirPresGenes1 does not exist. > >>>> > >>>> Regards > >>>> Christian > >>>> > >>>> > >>>> On 12/17/10 6:42 PM, Iain Gallagher > wrote: > >>>>> Hello List > >>>>> > >>>>> I wonder if someone would help me with > the > >> following > >>>> function. > >>>>> > >>>>> cumulMetric<- > function(deMirPresGenes, > >> deMirs){ > >>>>> > >>>>> #need to match position of each miR > in > >> deMirPresGenes > >>>> with its FC to form a vector of FC in > correct > >> order > >>>>>? ? ? ? fc<- > deMirs > >>>>>? ? ? ? > fcVector<- > >> as.numeric(with (fc, > >>>> FC[match(deMirPresGenes1[,4], Probe)] ) ) > >>>>> > >>>>>? ? ? ? #multiply > fc by context > >> score for > >>>> each interaction > >>>>>? ? ? ? metric<- > fcVector * > >>>> as.numeric(deMirPresGenes[,11]) > >>>>>? ? ? ? > geneMetric<- > >>>> cbind(deMirPresGenes[,2], > as.numeric(metric)) > >>>>> > >>>>>? ? ? ? > ???#make > >> cumul > >>>> weighted score > >>>>>? ? ? ? > listMetric<- > >> unstack(geneMetric, > >>>> > as.numeric(geneMetric[,2])~geneMetric[,1]) > >>>>>? ? ? ? > listMetric<- > >>>> as.data.frame(sapply(listMetric,sum)) > #returns a > >> dataframe > >>>>>? ? ? ? > colnames(listMetric)<- > >>>> c('cumulMetric') > >>>>> > >>>>>? ? ? ? #return > whole list > >>>>>? ? ? ? > return(listMetric) > >>>>> } > >>>>> > >>>>> deMirPresGenes looks like this: > >>>>> > >>>>> Gene.ID > >>>> Gene.Symbol? ? Species.ID > >>>> miRNA? ? Site.type > >>>> UTR_start? ? UTR_end > >>>> X3pairing_contr > >>>> local_AU_contr > >>>> position_contr > >>>> context_score? ? > context_percentile > >>>>> 22848? ? AAK1 > >>>> 9606? ? hsa-miR-183 > >>>> 2? ? 1546 > >>>> 1552? ? -0.026 > >>>> -0.047? ? 0.099 > >>>> -0.135? ? 47 > >>>>> 19? ? ABCA1 > >>>> 9606? ? hsa-miR-183 > >>>> 2? ? 1366 > >>>> 1372? ? -0.011 > >>>> -0.048? ? 0.087 > >>>> -0.133? ? 46 > >>>>> 20? ? ABCA2 > >>>> 9606? ? hsa-miR-495 > >>>> 2? ? 666 > >>>> 672? ? -0.042 > >>>> -0.092? ? -0.035 > >>>> -0.33? ? 93 > >>>>> 23456? ? ABCB10 > >>>> 9606? ? hsa-miR-183 > >>>> 3? ? 1475 > >>>> 1481? ? 0.003 > >>>> -0.109? ? -0.05 > >>>> -0.466? ? 98 > >>>>> 6059? ? ABCE1 > >>>> 9606? ? hsa-miR-495 > >>>> 2? ? 1474 > >>>> 1480? ? 0.005 > >>>> -0.046? ? 0.006 > >>>> -0.196? ? 58 > >>>>> 55324? ? ABCF3 > >>>> 9606? ? hsa-miR-1275 > >>>> 3? ? 90 > >>>> 96? ? 0.007 > >>>> 0.042? ? -0.055 > >>>> -0.316? ? 94 > >>>>> > >>>>> > >>>>> The aim of the function is to extract > a > >> dataframe of > >>>> gene symbols along with a weighted score > from the > >> above > >>>> data. The weighted score is the FC column > of > >> deMirs * the > >>>> context_score column of deMirPresGenes. > This is > >> easy peasy! > >>>>> > >>>>> Where I'm falling down is that if I > run this > >> function > >>>> it complains that 'geneMetric' can't be > found. Hmm > >> - I've > >>>> run it all line by line (i.e. not as a > function) > >> and it > >>>> works but wrapped up like this it fails! > >>>>> > >>>>> e.g. > >>>>> > >>>>>> testF2<- cumulMetric(testF1, > >> deMirs$up) > >>>>> Error in eval(expr, envir, enclos) : > object > >>>> 'geneMetric' not found > >>>>> > >>>>> deMirs$up looks like this: > >>>>> > >>>>> Probe? ? FC > >>>>> hsa-miR-183? ? 2.63 > >>>>> hsa-miR-1275? ? 2.74 > >>>>> hsa-miR-495? ? 3.13 > >>>>> hsa-miR-886-3p? ? 3.73 > >>>>> hsa-miR-886-5p? ? 3.97 > >>>>> hsa-miR-144*? ? 6.62 > >>>>> hsa-miR-451? ? 7.94 > >>>>> > >>>>> Could someone possibly point out where > I > >> falling > >>>> down. > >>>>> > >>>>> Thanks > >>>>> > >>>>> i > >>>>> > >>>>>> sessionInfo() > >>>>> R version 2.12.0 (2010-10-15) > >>>>> Platform: x86_64-pc-linux-gnu > (64-bit) > >>>>> > >>>>> locale: > >>>>>? ? ???[1] > >> LC_CTYPE=en_GB.utf8 > >>>>? ? > ???LC_NUMERIC=C > >>>>>? ? ???[3] > >> LC_TIME=en_GB.utf8 > >>>>? ? ? ? > LC_COLLATE=en_GB.utf8 > >>>>>? ? ???[5] > LC_MONETARY=C > >>>> > >>? ???LC_MESSAGES=en_GB.utf8 > >>>>>? ? ???[7] > >> LC_PAPER=en_GB.utf8 > >>>>? ? ???LC_NAME=C > >>>>>? ? ???[9] > LC_ADDRESS=C > >>>>? ? ? ? ? ? > LC_TELEPHONE=C > >>>>> [11] LC_MEASUREMENT=en_GB.utf8 > >> LC_IDENTIFICATION=C > >>>>> > >>>>> attached base packages: > >>>>> [1] stats? > ???graphics > >>>> grDevices utils? > ???datasets > >>>> methods???base > >>>>> > >>>>> loaded via a namespace (and not > attached): > >>>>> [1] tools_2.12.0 > >>>>>> > >>>>> > >>>>> > >> _______________________________________________ > >>>>> Bioconductor mailing list > >>>>> Bioconductor at r-project.org > >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >>>>> > >>>> > >>> > >>> > _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > >> > > >
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ok... done. Not really any further forward here. print statements after creating fcVector, metric and geneMetric (see output below). They all look ok in terms of structure and length. But the error persists and listMetric is not made?!?! Odd. I have added some comments to the output below. > tf2<-cumulMetric(tf1, deMirs$up)#deMirs$up is a dataframe (see prev posts) [1] 2.63 2.63 3.13 2.63 3.13 2.74 # print fcVector - looks ok [1] -0.35505 -0.34979 -1.03290 -1.22558 -0.61348 -0.86584 # print metric - looks ok [1] 1045 # lengthof metric - is correct sym metric # print geneMetric - looks ok [1,] "AAK1" "-0.35505" [2,] "ABCA1" "-0.34979" [3,] "ABCA2" "-1.0329" [4,] "ABCB10" "-1.22558" [5,] "ABCE1" "-0.61348" [6,] "ABCF3" "-0.86584" [1] 1045 # nrow of geneMetric - is correct Error in eval(expr, envir, enclos) : object 'geneMetric' not found > cheers i --- On Fri, 17/12/10, cstrato <cstrato at="" aon.at=""> wrote: > From: cstrato <cstrato at="" aon.at=""> > Subject: Re: [BioC] problem with function > To: "Iain Gallagher" <iaingallagher at="" btopenworld.com=""> > Cc: "bioconductor" <bioconductor at="" stat.math.ethz.ch=""> > Date: Friday, 17 December, 2010, 22:38 > At the moment I have no idea, but > what I would do in this case is to put > print() statements after each line to see where it fails. > > Christian > > On 12/17/10 10:59 PM, Iain Gallagher wrote: > > Hi > > > > FC is the second column of the deMirs variable. deMirs > is a dataframe with 2 columns - Probe (e.g. hsa-miR-145) and > FC (e.g 1.45). Using 'with' allows me to use deMirs as an > 'environment'. I thus don't have to pass FC explicitly. > > > > Cheers > > > > i > > > > --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at="">? > wrote: > > > >> From: cstrato<cstrato at="" aon.at=""> > >> Subject: Re: [BioC] problem with function > >> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> > >> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> > >> Date: Friday, 17 December, 2010, 20:39 > >> What is FC[]?? It is not passed > >> to the function. Christan > >> > >> On 12/17/10 8:11 PM, Iain Gallagher wrote: > >>> Sorry. > >>> > >>> That was a typo. In my script > deMirPresGenes1[,4] is > >> deMirPresGenes[,4]. > >>> > >>> Just to be sure I'm going about this the right > way > >> though I should say that at the moment I assign > the output > >> of another function to a variable called 'tf1' - > this object > >> is the same as the deMirPresGenes is my previous > email. > >>> > >>> This is then fed to my problem function using > >> positional matching. > >>> > >>> e.g. tf2<- cumulMetric(tf1, deMirs) > >>> > >>> Which leads to: > >>> > >>> Error in eval(expr, envir, enclos) : object > >> 'geneMetric' not found > >>> > >>> Hey ho! > >>> > >>> i > >>> > >>> --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at=""> > >> wrote: > >>> > >>>> From: cstrato<cstrato at="" aon.at=""> > >>>> Subject: Re: [BioC] problem with function > >>>> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> > >>>> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> > >>>> Date: Friday, 17 December, 2010, 18:40 > >>>> I am not sure but I would say that > >>>> deMirPresGenes1 does not exist. > >>>> > >>>> Regards > >>>> Christian > >>>> > >>>> > >>>> On 12/17/10 6:42 PM, Iain Gallagher > wrote: > >>>>> Hello List > >>>>> > >>>>> I wonder if someone would help me with > the > >> following > >>>> function. > >>>>> > >>>>> cumulMetric<- > function(deMirPresGenes, > >> deMirs){ > >>>>> > >>>>> #need to match position of each miR > in > >> deMirPresGenes > >>>> with its FC to form a vector of FC in > correct > >> order > >>>>>? ? ? ? fc<- > deMirs > >>>>>? ? ? ? > fcVector<- > >> as.numeric(with (fc, > >>>> FC[match(deMirPresGenes1[,4], Probe)] ) ) > >>>>> > >>>>>? ? ? ? #multiply > fc by context > >> score for > >>>> each interaction > >>>>>? ? ? ? metric<- > fcVector * > >>>> as.numeric(deMirPresGenes[,11]) > >>>>>? ? ? ? > geneMetric<- > >>>> cbind(deMirPresGenes[,2], > as.numeric(metric)) > >>>>> > >>>>>? ? ? ? > ???#make > >> cumul > >>>> weighted score > >>>>>? ? ? ? > listMetric<- > >> unstack(geneMetric, > >>>> > as.numeric(geneMetric[,2])~geneMetric[,1]) > >>>>>? ? ? ? > listMetric<- > >>>> as.data.frame(sapply(listMetric,sum)) > #returns a > >> dataframe > >>>>>? ? ? ? > colnames(listMetric)<- > >>>> c('cumulMetric') > >>>>> > >>>>>? ? ? ? #return > whole list > >>>>>? ? ? ? > return(listMetric) > >>>>> } > >>>>> > >>>>> deMirPresGenes looks like this: > >>>>> > >>>>> Gene.ID > >>>> Gene.Symbol? ? Species.ID > >>>> miRNA? ? Site.type > >>>> UTR_start? ? UTR_end > >>>> X3pairing_contr > >>>> local_AU_contr > >>>> position_contr > >>>> context_score? ? > context_percentile > >>>>> 22848? ? AAK1 > >>>> 9606? ? hsa-miR-183 > >>>> 2? ? 1546 > >>>> 1552? ? -0.026 > >>>> -0.047? ? 0.099 > >>>> -0.135? ? 47 > >>>>> 19? ? ABCA1 > >>>> 9606? ? hsa-miR-183 > >>>> 2? ? 1366 > >>>> 1372? ? -0.011 > >>>> -0.048? ? 0.087 > >>>> -0.133? ? 46 > >>>>> 20? ? ABCA2 > >>>> 9606? ? hsa-miR-495 > >>>> 2? ? 666 > >>>> 672? ? -0.042 > >>>> -0.092? ? -0.035 > >>>> -0.33? ? 93 > >>>>> 23456? ? ABCB10 > >>>> 9606? ? hsa-miR-183 > >>>> 3? ? 1475 > >>>> 1481? ? 0.003 > >>>> -0.109? ? -0.05 > >>>> -0.466? ? 98 > >>>>> 6059? ? ABCE1 > >>>> 9606? ? hsa-miR-495 > >>>> 2? ? 1474 > >>>> 1480? ? 0.005 > >>>> -0.046? ? 0.006 > >>>> -0.196? ? 58 > >>>>> 55324? ? ABCF3 > >>>> 9606? ? hsa-miR-1275 > >>>> 3? ? 90 > >>>> 96? ? 0.007 > >>>> 0.042? ? -0.055 > >>>> -0.316? ? 94 > >>>>> > >>>>> > >>>>> The aim of the function is to extract > a > >> dataframe of > >>>> gene symbols along with a weighted score > from the > >> above > >>>> data. The weighted score is the FC column > of > >> deMirs * the > >>>> context_score column of deMirPresGenes. > This is > >> easy peasy! > >>>>> > >>>>> Where I'm falling down is that if I > run this > >> function > >>>> it complains that 'geneMetric' can't be > found. Hmm > >> - I've > >>>> run it all line by line (i.e. not as a > function) > >> and it > >>>> works but wrapped up like this it fails! > >>>>> > >>>>> e.g. > >>>>> > >>>>>> testF2<- cumulMetric(testF1, > >> deMirs$up) > >>>>> Error in eval(expr, envir, enclos) : > object > >>>> 'geneMetric' not found > >>>>> > >>>>> deMirs$up looks like this: > >>>>> > >>>>> Probe? ? FC > >>>>> hsa-miR-183? ? 2.63 > >>>>> hsa-miR-1275? ? 2.74 > >>>>> hsa-miR-495? ? 3.13 > >>>>> hsa-miR-886-3p? ? 3.73 > >>>>> hsa-miR-886-5p? ? 3.97 > >>>>> hsa-miR-144*? ? 6.62 > >>>>> hsa-miR-451? ? 7.94 > >>>>> > >>>>> Could someone possibly point out where > I > >> falling > >>>> down. > >>>>> > >>>>> Thanks > >>>>> > >>>>> i > >>>>> > >>>>>> sessionInfo() > >>>>> R version 2.12.0 (2010-10-15) > >>>>> Platform: x86_64-pc-linux-gnu > (64-bit) > >>>>> > >>>>> locale: > >>>>>? ? ???[1] > >> LC_CTYPE=en_GB.utf8 > >>>>? ? > ???LC_NUMERIC=C > >>>>>? ? ???[3] > >> LC_TIME=en_GB.utf8 > >>>>? ? ? ? > LC_COLLATE=en_GB.utf8 > >>>>>? ? ???[5] > LC_MONETARY=C > >>>> > >>? ???LC_MESSAGES=en_GB.utf8 > >>>>>? ? ???[7] > >> LC_PAPER=en_GB.utf8 > >>>>? ? ???LC_NAME=C > >>>>>? ? ???[9] > LC_ADDRESS=C > >>>>? ? ? ? ? ? > LC_TELEPHONE=C > >>>>> [11] LC_MEASUREMENT=en_GB.utf8 > >> LC_IDENTIFICATION=C > >>>>> > >>>>> attached base packages: > >>>>> [1] stats? > ???graphics > >>>> grDevices utils? > ???datasets > >>>> methods???base > >>>>> > >>>>> loaded via a namespace (and not > attached): > >>>>> [1] tools_2.12.0 > >>>>>> > >>>>> > >>>>> > >> _______________________________________________ > >>>>> Bioconductor mailing list > >>>>> Bioconductor at r-project.org > >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >>>>> > >>>> > >>> > >>> > _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > >> > > >
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You need to do: cumulMetric <- function(deMirPresGenes, deMirs){ fc <- deMirs fcVector <- as.numeric(with (fc, FC[match(deMirPresGenes[,4], Probe)] ) ) metric <- fcVector * as.numeric(deMirPresGenes[,11]) geneMetric <- as.data.frame(cbind(deMirPresGenes[,2], as.numeric(metric))) colnames(geneMetric) <- c('y', 'x') listMetric <- unstack(geneMetric, x ~ y) listMetric <- as.data.frame(sapply(listMetric,sum)) #returns a dataframe colnames(listMetric) <- c('cumulMetric') return(listMetric) } Regards Christian On 12/17/10 11:52 PM, Iain Gallagher wrote: > ok... done. Not really any further forward here. > > print statements after creating fcVector, metric and geneMetric (see output below). They all look ok in terms of structure and length. But the error persists and listMetric is not made?!?! Odd. > > I have added some comments to the output below. > >> tf2<-cumulMetric(tf1, deMirs$up)#deMirs$up is a dataframe (see prev posts) > [1] 2.63 2.63 3.13 2.63 3.13 2.74 # print fcVector - looks ok > [1] -0.35505 -0.34979 -1.03290 -1.22558 -0.61348 -0.86584 # print metric - looks ok > [1] 1045 # lengthof metric - is correct > sym metric # print geneMetric - looks ok > [1,] "AAK1" "-0.35505" > [2,] "ABCA1" "-0.34979" > [3,] "ABCA2" "-1.0329" > [4,] "ABCB10" "-1.22558" > [5,] "ABCE1" "-0.61348" > [6,] "ABCF3" "-0.86584" > [1] 1045 # nrow of geneMetric - is correct > Error in eval(expr, envir, enclos) : object 'geneMetric' not found >> > > cheers > > i > --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at=""> wrote: > >> From: cstrato<cstrato at="" aon.at=""> >> Subject: Re: [BioC] problem with function >> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> >> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> >> Date: Friday, 17 December, 2010, 22:38 >> At the moment I have no idea, but >> what I would do in this case is to put >> print() statements after each line to see where it fails. >> >> Christian >> >> On 12/17/10 10:59 PM, Iain Gallagher wrote: >>> Hi >>> >>> FC is the second column of the deMirs variable. deMirs >> is a dataframe with 2 columns - Probe (e.g. hsa-miR-145) and >> FC (e.g 1.45). Using 'with' allows me to use deMirs as an >> 'environment'. I thus don't have to pass FC explicitly. >>> >>> Cheers >>> >>> i >>> >>> --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at=""> >> wrote: >>> >>>> From: cstrato<cstrato at="" aon.at=""> >>>> Subject: Re: [BioC] problem with function >>>> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> >>>> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> >>>> Date: Friday, 17 December, 2010, 20:39 >>>> What is FC[]? It is not passed >>>> to the function. Christan >>>> >>>> On 12/17/10 8:11 PM, Iain Gallagher wrote: >>>>> Sorry. >>>>> >>>>> That was a typo. In my script >> deMirPresGenes1[,4] is >>>> deMirPresGenes[,4]. >>>>> >>>>> Just to be sure I'm going about this the right >> way >>>> though I should say that at the moment I assign >> the output >>>> of another function to a variable called 'tf1' - >> this object >>>> is the same as the deMirPresGenes is my previous >> email. >>>>> >>>>> This is then fed to my problem function using >>>> positional matching. >>>>> >>>>> e.g. tf2<- cumulMetric(tf1, deMirs) >>>>> >>>>> Which leads to: >>>>> >>>>> Error in eval(expr, envir, enclos) : object >>>> 'geneMetric' not found >>>>> >>>>> Hey ho! >>>>> >>>>> i >>>>> >>>>> --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at=""> >>>> wrote: >>>>> >>>>>> From: cstrato<cstrato at="" aon.at=""> >>>>>> Subject: Re: [BioC] problem with function >>>>>> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> >>>>>> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> >>>>>> Date: Friday, 17 December, 2010, 18:40 >>>>>> I am not sure but I would say that >>>>>> deMirPresGenes1 does not exist. >>>>>> >>>>>> Regards >>>>>> Christian >>>>>> >>>>>> >>>>>> On 12/17/10 6:42 PM, Iain Gallagher >> wrote: >>>>>>> Hello List >>>>>>> >>>>>>> I wonder if someone would help me with >> the >>>> following >>>>>> function. >>>>>>> >>>>>>> cumulMetric<- >> function(deMirPresGenes, >>>> deMirs){ >>>>>>> >>>>>>> #need to match position of each miR >> in >>>> deMirPresGenes >>>>>> with its FC to form a vector of FC in >> correct >>>> order >>>>>>> fc<- >> deMirs >>>>>>> >> fcVector<- >>>> as.numeric(with (fc, >>>>>> FC[match(deMirPresGenes1[,4], Probe)] ) ) >>>>>>> >>>>>>> #multiply >> fc by context >>>> score for >>>>>> each interaction >>>>>>> metric<- >> fcVector * >>>>>> as.numeric(deMirPresGenes[,11]) >>>>>>> >> geneMetric<- >>>>>> cbind(deMirPresGenes[,2], >> as.numeric(metric)) >>>>>>> >>>>>>> >> #make >>>> cumul >>>>>> weighted score >>>>>>> >> listMetric<- >>>> unstack(geneMetric, >>>>>> >> as.numeric(geneMetric[,2])~geneMetric[,1]) >>>>>>> >> listMetric<- >>>>>> as.data.frame(sapply(listMetric,sum)) >> #returns a >>>> dataframe >>>>>>> >> colnames(listMetric)<- >>>>>> c('cumulMetric') >>>>>>> >>>>>>> #return >> whole list >>>>>>> >> return(listMetric) >>>>>>> } >>>>>>> >>>>>>> deMirPresGenes looks like this: >>>>>>> >>>>>>> Gene.ID >>>>>> Gene.Symbol Species.ID >>>>>> miRNA Site.type >>>>>> UTR_start UTR_end >>>>>> X3pairing_contr >>>>>> local_AU_contr >>>>>> position_contr >>>>>> context_score >> context_percentile >>>>>>> 22848 AAK1 >>>>>> 9606 hsa-miR-183 >>>>>> 2 1546 >>>>>> 1552 -0.026 >>>>>> -0.047 0.099 >>>>>> -0.135 47 >>>>>>> 19 ABCA1 >>>>>> 9606 hsa-miR-183 >>>>>> 2 1366 >>>>>> 1372 -0.011 >>>>>> -0.048 0.087 >>>>>> -0.133 46 >>>>>>> 20 ABCA2 >>>>>> 9606 hsa-miR-495 >>>>>> 2 666 >>>>>> 672 -0.042 >>>>>> -0.092 -0.035 >>>>>> -0.33 93 >>>>>>> 23456 ABCB10 >>>>>> 9606 hsa-miR-183 >>>>>> 3 1475 >>>>>> 1481 0.003 >>>>>> -0.109 -0.05 >>>>>> -0.466 98 >>>>>>> 6059 ABCE1 >>>>>> 9606 hsa-miR-495 >>>>>> 2 1474 >>>>>> 1480 0.005 >>>>>> -0.046 0.006 >>>>>> -0.196 58 >>>>>>> 55324 ABCF3 >>>>>> 9606 hsa-miR-1275 >>>>>> 3 90 >>>>>> 96 0.007 >>>>>> 0.042 -0.055 >>>>>> -0.316 94 >>>>>>> >>>>>>> >>>>>>> The aim of the function is to extract >> a >>>> dataframe of >>>>>> gene symbols along with a weighted score >> from the >>>> above >>>>>> data. The weighted score is the FC column >> of >>>> deMirs * the >>>>>> context_score column of deMirPresGenes. >> This is >>>> easy peasy! >>>>>>> >>>>>>> Where I'm falling down is that if I >> run this >>>> function >>>>>> it complains that 'geneMetric' can't be >> found. Hmm >>>> - I've >>>>>> run it all line by line (i.e. not as a >> function) >>>> and it >>>>>> works but wrapped up like this it fails! >>>>>>> >>>>>>> e.g. >>>>>>> >>>>>>>> testF2<- cumulMetric(testF1, >>>> deMirs$up) >>>>>>> Error in eval(expr, envir, enclos) : >> object >>>>>> 'geneMetric' not found >>>>>>> >>>>>>> deMirs$up looks like this: >>>>>>> >>>>>>> Probe FC >>>>>>> hsa-miR-183 2.63 >>>>>>> hsa-miR-1275 2.74 >>>>>>> hsa-miR-495 3.13 >>>>>>> hsa-miR-886-3p 3.73 >>>>>>> hsa-miR-886-5p 3.97 >>>>>>> hsa-miR-144* 6.62 >>>>>>> hsa-miR-451 7.94 >>>>>>> >>>>>>> Could someone possibly point out where >> I >>>> falling >>>>>> down. >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> i >>>>>>> >>>>>>>> sessionInfo() >>>>>>> R version 2.12.0 (2010-10-15) >>>>>>> Platform: x86_64-pc-linux-gnu >> (64-bit) >>>>>>> >>>>>>> locale: >>>>>>> [1] >>>> LC_CTYPE=en_GB.utf8 >>>>>> >> LC_NUMERIC=C >>>>>>> [3] >>>> LC_TIME=en_GB.utf8 >>>>>> >> LC_COLLATE=en_GB.utf8 >>>>>>> [5] >> LC_MONETARY=C >>>>>> >>>> LC_MESSAGES=en_GB.utf8 >>>>>>> [7] >>>> LC_PAPER=en_GB.utf8 >>>>>> LC_NAME=C >>>>>>> [9] >> LC_ADDRESS=C >>>>>> >> LC_TELEPHONE=C >>>>>>> [11] LC_MEASUREMENT=en_GB.utf8 >>>> LC_IDENTIFICATION=C >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] stats >> graphics >>>>>> grDevices utils >> datasets >>>>>> methods base >>>>>>> >>>>>>> loaded via a namespace (and not >> attached): >>>>>>> [1] tools_2.12.0 >>>>>>>> >>>>>>> >>>>>>> >>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at r-project.org >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>>> >>>>> >>>>> >> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>> >>> >> >
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Entering edit mode
@iain-gallagher-2532
Last seen 8.7 years ago
United Kingdom
Hi Christian, Chuck (and lists) It seems that the problem may be the strange behaviour of 'unstack' inside a function. See this thread in the R mailing list: http://tolstoy.newcastle.edu.au/R/help/04/03/1160.html Anyway, I got round the problem by using 'aggregate' instead of converting to a list and then tapply to sum values of metric. Probably more efficient as well. Thanks for the help offered. My function now looks like this (for the record!) and behaves as it should. makeMetric <- function(deMirPresGenes, deMirs){ ??? #need to match position of each miR in deMirPresGenes with its FC to form a vector of FC in correct order ??? ??? fcVector <- as.numeric(with (deMirs, FC[match(deMirPresGenes[,4], Probe)] ) ) ??? #multiply fc by context score for each interaction??? ? ? metric <- fcVector * as.numeric(deMirPresGenes[,11]) ? ? geneMetric <- cbind(deMirPresGenes[,2], metric) ? ? colnames(geneMetric) <- c('sym', 'metric') ? ? ? ? #make cumul by aggregate ? ? listMetric <- aggregate(as.numeric(geneMetric[,2]), list(geneMetric[,1]), sum)#returns a dataframe ??? colnames(listMetric) <- c('symbol','cumulMetric') ? ? ??? #return whole list ??? return(listMetric)# dataframe } Cheers i --- On Sat, 18/12/10, cstrato <cstrato at="" aon.at=""> wrote: > From: cstrato <cstrato at="" aon.at=""> > Subject: Re: [BioC] problem with function > To: "Iain Gallagher" <iaingallagher at="" btopenworld.com=""> > Cc: "bioconductor" <bioconductor at="" stat.math.ethz.ch=""> > Date: Saturday, 18 December, 2010, 14:40 > You need to do: > > cumulMetric <- function(deMirPresGenes, deMirs){ > ??? fc <- deMirs > ??? fcVector <- as.numeric(with (fc, > FC[match(deMirPresGenes[,4], Probe)] ) ) > > ??? metric <- fcVector * > as.numeric(deMirPresGenes[,11]) > ??? geneMetric <- > as.data.frame(cbind(deMirPresGenes[,2], > as.numeric(metric))) > ??? colnames(geneMetric) <- c('y', 'x') > > ??? listMetric <- unstack(geneMetric, x ~ > y) > ??? listMetric <- > as.data.frame(sapply(listMetric,sum)) #returns a dataframe > ??? colnames(listMetric) <- > c('cumulMetric') > > ??? return(listMetric) > } > > Regards > Christian > > On 12/17/10 11:52 PM, Iain Gallagher wrote: > > ok... done. Not really any further forward here. > > > > print statements after creating fcVector, metric and > geneMetric (see output below). They all look ok in terms of > structure and length. But the error persists and listMetric > is not made?!?! Odd. > > > > I have added some comments to the output below. > > > >> tf2<-cumulMetric(tf1, deMirs$up)#deMirs$up is a > dataframe (see prev posts) > > [1] 2.63 2.63 3.13 2.63 3.13 2.74 # print fcVector - > looks ok > > [1] -0.35505 -0.34979 -1.03290 -1.22558 -0.61348 > -0.86584 # print metric - looks ok > > [1] 1045 # lengthof metric - is correct > >? ? ???sym? ? ? > metric? ? # print geneMetric - looks ok > > [1,] "AAK1"???"-0.35505" > > [2,] "ABCA1"? "-0.34979" > > [3,] "ABCA2"? "-1.0329" > > [4,] "ABCB10" "-1.22558" > > [5,] "ABCE1"? "-0.61348" > > [6,] "ABCF3"? "-0.86584" > > [1] 1045 # nrow of geneMetric - is correct > > Error in eval(expr, envir, enclos) : object > 'geneMetric' not found > >> > > > > cheers > > > > i > > --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at="">? > wrote: > > > >> From: cstrato<cstrato at="" aon.at=""> > >> Subject: Re: [BioC] problem with function > >> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> > >> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> > >> Date: Friday, 17 December, 2010, 22:38 > >> At the moment I have no idea, but > >> what I would do in this case is to put > >> print() statements after each line to see where it > fails. > >> > >> Christian > >> > >> On 12/17/10 10:59 PM, Iain Gallagher wrote: > >>> Hi > >>> > >>> FC is the second column of the deMirs > variable. deMirs > >> is a dataframe with 2 columns - Probe (e.g. > hsa-miR-145) and > >> FC (e.g 1.45). Using 'with' allows me to use > deMirs as an > >> 'environment'. I thus don't have to pass FC > explicitly. > >>> > >>> Cheers > >>> > >>> i > >>> > >>> --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at=""> > >> wrote: > >>> > >>>> From: cstrato<cstrato at="" aon.at=""> > >>>> Subject: Re: [BioC] problem with function > >>>> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> > >>>> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> > >>>> Date: Friday, 17 December, 2010, 20:39 > >>>> What is FC[]?? It is not passed > >>>> to the function. Christan > >>>> > >>>> On 12/17/10 8:11 PM, Iain Gallagher > wrote: > >>>>> Sorry. > >>>>> > >>>>> That was a typo. In my script > >> deMirPresGenes1[,4] is > >>>> deMirPresGenes[,4]. > >>>>> > >>>>> Just to be sure I'm going about this > the right > >> way > >>>> though I should say that at the moment I > assign > >> the output > >>>> of another function to a variable called > 'tf1' - > >> this object > >>>> is the same as the deMirPresGenes is my > previous > >> email. > >>>>> > >>>>> This is then fed to my problem > function using > >>>> positional matching. > >>>>> > >>>>> e.g. tf2<- cumulMetric(tf1, > deMirs) > >>>>> > >>>>> Which leads to: > >>>>> > >>>>> Error in eval(expr, envir, enclos) : > object > >>>> 'geneMetric' not found > >>>>> > >>>>> Hey ho! > >>>>> > >>>>> i > >>>>> > >>>>> --- On Fri, 17/12/10, cstrato<cstrato at="" aon.at=""> > >>>> wrote: > >>>>> > >>>>>> From: cstrato<cstrato at="" aon.at=""> > >>>>>> Subject: Re: [BioC] problem with > function > >>>>>> To: "Iain Gallagher"<iaingallagher at="" btopenworld.com=""> > >>>>>> Cc: "bioconductor"<bioconductor at="" stat.math.ethz.ch=""> > >>>>>> Date: Friday, 17 December, 2010, > 18:40 > >>>>>> I am not sure but I would say > that > >>>>>> deMirPresGenes1 does not exist. > >>>>>> > >>>>>> Regards > >>>>>> Christian > >>>>>> > >>>>>> > >>>>>> On 12/17/10 6:42 PM, Iain > Gallagher > >> wrote: > >>>>>>> Hello List > >>>>>>> > >>>>>>> I wonder if someone would help > me with > >> the > >>>> following > >>>>>> function. > >>>>>>> > >>>>>>> cumulMetric<- > >> function(deMirPresGenes, > >>>> deMirs){ > >>>>>>> > >>>>>>> #need to match position of > each miR > >> in > >>>> deMirPresGenes > >>>>>> with its FC to form a vector of FC > in > >> correct > >>>> order > >>>>>>>? ? ? ? > ? fc<- > >> deMirs > >>>>>>> > >> fcVector<- > >>>> as.numeric(with (fc, > >>>>>> FC[match(deMirPresGenes1[,4], > Probe)] ) ) > >>>>>>> > >>>>>>>? ? ? ? > ? #multiply > >> fc by context > >>>> score for > >>>>>> each interaction > >>>>>>>? ? ? ? > ? metric<- > >> fcVector * > >>>>>> as.numeric(deMirPresGenes[,11]) > >>>>>>> > >> geneMetric<- > >>>>>> cbind(deMirPresGenes[,2], > >> as.numeric(metric)) > >>>>>>> > >>>>>>> > >>? ???#make > >>>> cumul > >>>>>> weighted score > >>>>>>> > >> listMetric<- > >>>> unstack(geneMetric, > >>>>>> > >> as.numeric(geneMetric[,2])~geneMetric[,1]) > >>>>>>> > >> listMetric<- > >>>>>> > as.data.frame(sapply(listMetric,sum)) > >> #returns a > >>>> dataframe > >>>>>>> > >> colnames(listMetric)<- > >>>>>> c('cumulMetric') > >>>>>>> > >>>>>>>? ? ? ? > ? #return > >> whole list > >>>>>>> > >> return(listMetric) > >>>>>>> } > >>>>>>> > >>>>>>> deMirPresGenes looks like > this: > >>>>>>> > >>>>>>> Gene.ID > >>>>>> Gene.Symbol? ? > Species.ID > >>>>>> miRNA? ? Site.type > >>>>>> UTR_start? ? UTR_end > >>>>>> X3pairing_contr > >>>>>> local_AU_contr > >>>>>> position_contr > >>>>>> context_score > >> context_percentile > >>>>>>> 22848? ? AAK1 > >>>>>> 9606? ? hsa-miR-183 > >>>>>> 2? ? 1546 > >>>>>> 1552? ? -0.026 > >>>>>> -0.047? ? 0.099 > >>>>>> -0.135? ? 47 > >>>>>>> 19? ? ABCA1 > >>>>>> 9606? ? hsa-miR-183 > >>>>>> 2? ? 1366 > >>>>>> 1372? ? -0.011 > >>>>>> -0.048? ? 0.087 > >>>>>> -0.133? ? 46 > >>>>>>> 20? ? ABCA2 > >>>>>> 9606? ? hsa-miR-495 > >>>>>> 2? ? 666 > >>>>>> 672? ? -0.042 > >>>>>> -0.092? ? -0.035 > >>>>>> -0.33? ? 93 > >>>>>>> 23456? ? ABCB10 > >>>>>> 9606? ? hsa-miR-183 > >>>>>> 3? ? 1475 > >>>>>> 1481? ? 0.003 > >>>>>> -0.109? ? -0.05 > >>>>>> -0.466? ? 98 > >>>>>>> 6059? ? ABCE1 > >>>>>> 9606? ? hsa-miR-495 > >>>>>> 2? ? 1474 > >>>>>> 1480? ? 0.005 > >>>>>> -0.046? ? 0.006 > >>>>>> -0.196? ? 58 > >>>>>>> 55324? ? ABCF3 > >>>>>> 9606? ? hsa-miR-1275 > >>>>>> 3? ? 90 > >>>>>> 96? ? 0.007 > >>>>>> 0.042? ? -0.055 > >>>>>> -0.316? ? 94 > >>>>>>> > >>>>>>> > >>>>>>> The aim of the function is to > extract > >> a > >>>> dataframe of > >>>>>> gene symbols along with a weighted > score > >> from the > >>>> above > >>>>>> data. The weighted score is the FC > column > >> of > >>>> deMirs * the > >>>>>> context_score column of > deMirPresGenes. > >> This is > >>>> easy peasy! > >>>>>>> > >>>>>>> Where I'm falling down is that > if I > >> run this > >>>> function > >>>>>> it complains that 'geneMetric' > can't be > >> found. Hmm > >>>> - I've > >>>>>> run it all line by line (i.e. not > as a > >> function) > >>>> and it > >>>>>> works but wrapped up like this it > fails! > >>>>>>> > >>>>>>> e.g. > >>>>>>> > >>>>>>>> testF2<- > cumulMetric(testF1, > >>>> deMirs$up) > >>>>>>> Error in eval(expr, envir, > enclos) : > >> object > >>>>>> 'geneMetric' not found > >>>>>>> > >>>>>>> deMirs$up looks like this: > >>>>>>> > >>>>>>> Probe? ? FC > >>>>>>> hsa-miR-183? ? 2.63 > >>>>>>> hsa-miR-1275? ? > 2.74 > >>>>>>> hsa-miR-495? ? 3.13 > >>>>>>> hsa-miR-886-3p? ? > 3.73 > >>>>>>> hsa-miR-886-5p? ? > 3.97 > >>>>>>> hsa-miR-144*? ? > 6.62 > >>>>>>> hsa-miR-451? ? 7.94 > >>>>>>> > >>>>>>> Could someone possibly point > out where > >> I > >>>> falling > >>>>>> down. > >>>>>>> > >>>>>>> Thanks > >>>>>>> > >>>>>>> i > >>>>>>> > >>>>>>>> sessionInfo() > >>>>>>> R version 2.12.0 (2010-10-15) > >>>>>>> Platform: x86_64-pc-linux-gnu > >> (64-bit) > >>>>>>> > >>>>>>> locale: > >>>>>>>? ? ? > ???[1] > >>>> LC_CTYPE=en_GB.utf8 > >>>>>> > >>? ???LC_NUMERIC=C > >>>>>>>? ? ? > ???[3] > >>>> LC_TIME=en_GB.utf8 > >>>>>> > >> LC_COLLATE=en_GB.utf8 > >>>>>>>? ? ? > ???[5] > >> LC_MONETARY=C > >>>>>> > >>>>? ? > ???LC_MESSAGES=en_GB.utf8 > >>>>>>>? ? ? > ???[7] > >>>> LC_PAPER=en_GB.utf8 > >>>>>>? ? ? > ???LC_NAME=C > >>>>>>>? ? ? > ???[9] > >> LC_ADDRESS=C > >>>>>> > >> LC_TELEPHONE=C > >>>>>>> [11] > LC_MEASUREMENT=en_GB.utf8 > >>>> LC_IDENTIFICATION=C > >>>>>>> > >>>>>>> attached base packages: > >>>>>>> [1] stats > >>? ???graphics > >>>>>> grDevices utils > >>? ???datasets > >>>>>> methods???base > >>>>>>> > >>>>>>> loaded via a namespace (and > not > >> attached): > >>>>>>> [1] tools_2.12.0 > >>>>>>>> > >>>>>>> > >>>>>>> > >>>> > _______________________________________________ > >>>>>>> Bioconductor mailing list > >>>>>>> Bioconductor at r-project.org > >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >>>>>>> > >>>>>> > >>>>> > >>>>> > >> _______________________________________________ > >>>>> Bioconductor mailing list > >>>>> Bioconductor at r-project.org > >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >>>>> > >>>> > >>> > >> > > >
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