Question: genotyping output files
0
gravatar for Rafiq S.
7.6 years ago by
Rafiq S.20
Rafiq S.20 wrote:
Dear All, I have recently attempted a genome wide genotyping experiment on around 500 samples using the Illumina 660quad chip. Crlmm genotyping was completed and a snpset object crlmmResult was created. I have used the calls(crlmmResult) and the configuation command to quickly browse through the genotypes. I was expecting that at the end of the process crlmm would produce a text file with all the genotypes which could be transported to other softwares like plink for association analysis, This hasnt happened and a text file was not generated, however a crlmmResult.Rda file was extracted into SNPchip packages in my rlibrary. Could you please direct me towards what other prrocesses which I might need to complete before I can obtain an output text file all the with genome wide calls? Many Thanks, -S
process snpchip crlmm • 1.5k views
ADD COMMENTlink modified 7.6 years ago • written 7.6 years ago by Rafiq S.20
Answer: genotyping output files
0
gravatar for Rafiq S.
7.6 years ago by
Rafiq S.20
Rafiq S.20 wrote:
Dear All, I have recently attempted a genome wide genotyping experiment on around 500 samples using the Illumina 660quad chip. Crlmm genotyping was completed and a snpset object crlmmResult was created. I have used the calls(crlmmResult) and the configuation command to quickly browse through the genotypes. I was expecting that at the end of the process crlmm would produce a text file with all the genotypes which could be transported to other softwares like plink for association analysis, This hasnt happened and a text file was not generated, however a crlmmResult.Rda file was extracted into SNPchip packages in my rlibrary. Could you please direct me towards what other prrocesses which I might need to complete before I can obtain an output text file all the with genome wide calls? Many Thanks, -S
ADD COMMENTlink written 7.6 years ago by Rafiq S.20
Dear Rafiq S. You do not have to reissue your query. You can verify that it was broadcast by checking the mailing list archive. There are to my knowledge no immediate translations from crlmm output to plink input. The "downstream" vignette http://www.bioconductor.org/packages/2.9/bioc/vignettes/crlmm/inst/doc /crlmmDownstream.pdf shows some relevant conversions, but the document is obsolete and needs to be rebuilt. If you substitute "snpStats" for "snpMatrix" and "SnpMatrix" for "snp.matrix", everything should work as noted. You can use coercion of the SnpMatrix instance to "character" to get the calls in "A/B" format. On Sat, Jan 14, 2012 at 6:42 PM, Rafiq S. <s.rafiq at="" soton.ac.uk=""> wrote: > > Dear All, > > I have recently attempted a genome wide genotyping experiment on around 500 samples using the Illumina 660quad chip. > Crlmm genotyping was completed and a snpset object crlmmResult was created. > > I have used the calls(crlmmResult) and the configuation command to quickly browse through the genotypes. > > I was expecting that at the end of the process crlmm would produce a text file with all the genotypes which could be transported to other softwares like plink for association analysis, > This hasnt happened and a text file was not generated, ?however a crlmmResult.Rda file was extracted into SNPchip packages in my rlibrary. > > Could you please direct ?me towards what other prrocesses which I might ?need to complete before I can obtain an output text file all the with genome wide calls? > > Many Thanks, > > -S > > _______________________________________________ > 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
ADD REPLYlink written 7.6 years ago by Vincent J. Carey, Jr.6.3k
simply get the output of calls(crlmmResult), for example: theCalls = calls(crlmmResult) and write it out to a text file: write.table(theCalls, file='theCalls.txt', sep='\t', quote=FALSE) and this will create a tab-delimited file in which the rows are the SNPs and the columns are the samples. Note that the calls are coded 1 (AA), 2 (AB) and 3 (BB)... b On 14 January 2012 23:42, Rafiq S. <s.rafiq at="" soton.ac.uk=""> wrote: > > Dear All, > > I have recently attempted a genome wide genotyping experiment on around 500 samples using the Illumina 660quad chip. > Crlmm genotyping was completed and a snpset object crlmmResult was created. > > I have used the calls(crlmmResult) and the configuation command to quickly browse through the genotypes. > > I was expecting that at the end of the process crlmm would produce a text file with all the genotypes which could be transported to other softwares like plink for association analysis, > This hasnt happened and a text file was not generated, ?however a crlmmResult.Rda file was extracted into SNPchip packages in my rlibrary. > > Could you please direct ?me towards what other prrocesses which I might ?need to complete before I can obtain an output text file all the with genome wide calls? > > Many Thanks, > > -S > > _______________________________________________ > 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
ADD REPLYlink written 7.6 years ago by Benilton Carvalho4.3k
As I had this requirement just the other week with affy SNP 6 arrays, I made a small script to produce map and ped files. You probably need some changes for your particular situation , like selecting the correct columns from an annotation file. targets is a dataframe containing patient information. # Create map and ped file, use http://www.gwaspi.org/?page_id=145 as reference # Annotation from Affymetrix.com annot<-read.csv("annotationData/GenomeWideSNP_6.na32.annot.csv", skip=21,row.names=1,as.is=TRUE) # snp.index <- which(isSnp(cnSet) & !is.na(chromosome(cnSet))) calls<-assayData(cnSet)$call[snp.index,] # Create map file annot<-annot[rownames(calls),] # third column of mapfile (genetic position (cM) is not in annotation, take one that is mostly 0) mapfile<-annot[,c("Chromosome", "dbSNP.RS.ID","ChrX.pseudo.autosomal.region.1", "Physical.Position")] # Create ped file alleleA<-alleleB<-matrix("", nrow=nrow(calls), ncol=ncol(calls), dimnames=dimnames(calls)) # take complement of SNPs on reverse strand allA<-annot$Allele.A allComplA<-c("A","C","G","T")[match(allA,c("T","G","C","A"))] forwA<-ifelse(annot$Strand=="+",allA,allComplA) allB<-annot$Allele.B allComplB<-c("A","C","G","T")[match(allB,c("T","G","C","A"))] forwB<-ifelse(annot$Strand=="+",allB,allComplB) for (r in 1:ncol(calls)){ alleleA[,r]<-ifelse(calls[,r]<3,forwA,forwB) alleleB[,r]<-ifelse(calls[,r]<2,forwA,forwB) } ped<-matrix("",ncol=nrow(alleleA)*2+6,nrow=ncol(alleleA)) for (r in 1:ncol(calls)){ ped[r,(1:nrow(alleleA))*2+5]<-alleleA[,r] ped[r,(1:nrow(alleleB))*2+6]<-alleleB[,r] } # Family id ped[,1]<-targets$PatientId # sample id ped[,2]<-make.names(targets$DisplayLabel) # Paternal id, maternal id ped[,3:4]<-"0" # Gender (1=male, 2=female) ped[,5]<-ifelse(targets$Gender=="M","1","2") # Affection (0=unknown,1=unaffected, 2=affected) ped[,6]<-ifelse(targets$NorTum=="N","1","2") # write.table(mapfile, file="SNPollier.map", quote=FALSE, row.names=FALSE, col.names=FALSE) write.table(ped, file="SNPollier.ped", quote=FALSE, row.names=FALSE, col.names=FALSE) > > > Dear All, > > I have recently attempted a genome wide genotyping experiment on around > 500 samples using the Illumina 660quad chip. > Crlmm genotyping was completed and a snpset object crlmmResult was > created. > > I have used the calls(crlmmResult) and the configuation command to quickly > browse through the genotypes. > > I was expecting that at the end of the process crlmm would produce a text > file with all the genotypes which could be transported to other softwares > like plink for association analysis, > This hasnt happened and a text file was not generated, however a > crlmmResult.Rda file was extracted into SNPchip packages in my rlibrary. > > Could you please direct me towards what other prrocesses which I might > need to complete before I can obtain an output text file all the with > genome wide calls? >
ADD REPLYlink written 7.6 years ago by Oosting, J. PATH550
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