shift function (GenomicRanges, IRanges), issue with negative start values and circular DNA
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@ivanek-robert-3765
Last seen 10.2 years ago
## ################################################################### ########## ## library("GenomicRanges") ## Loading required package: IRanges ## Attaching package: ‘IRanges’ ## The following object(s) are masked from ‘package:base’: ## cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union ## ## ################################################################### ########## ## chr1.gr <- GRanges(seqnames=Rle("chr1", 4), ranges=IRanges(start=rep(c(1,197195432),each=2), width=1), strand=rep(c("+","-"),2), seqlengths=c(chr1=197195432)) ## isCircularchr1.gr) <- FALSE ## chr1.gr ## GRanges with 4 ranges and 0 elementMetadata values: ## seqnames ranges strand ## <rle> <iranges> <rle> ## [1] chr1 [ 1, 1] + ## [2] chr1 [ 1, 1] - ## [3] chr1 [197195432, 197195432] + ## [4] chr1 [197195432, 197195432] - ## --- ## seqlengths: ## chr1 ## 197195432 ## seqinfochr1.gr) ## Seqinfo of length 1 ## seqnames seqlengths isCircular ## chr1 197195432 FALSE ## shiftchr1.gr, shift=50) ## GRanges with 4 ranges and 0 elementMetadata values: ## seqnames ranges strand ## <rle> <iranges> <rle> ## [1] chr1 [ 51, 51] + ## [2] chr1 [ 51, 51] - ## [3] chr1 [197195432, 197195432] + ## [4] chr1 [197195432, 197195432] - ## --- ## seqlengths: ## chr1 ## 197195432 ## Warning message: ## In `end<-`(`*tmp*`, check = FALSE, value = c(51L, 51L, 197195482L, : ## trimmed end values to be <= seqlengths ## shiftchr1.gr, shift=50 * as.integerifelsestrandchr1.gr)=="-", -1, 1))) ## Error in validObject(x) : ## invalid class “IRanges” object: 'widths(x)' cannot contain negative values ## In addition: Warning messages: ## 1: In `end<-`(`*tmp*`, check = FALSE, value = c(51L, -49L, 197195482L, : ## trimmed end values to be <= seqlengths ## 2: In `start<-`(`*tmp*`, value = c(51L, -49L, 197195432L, 197195382L : ## trimmed start values to be positive ## ## ################################################################### ########## ## chrM.gr <- GRanges(seqnames=Rle("chrM", 4), ranges=IRanges(start=rep(c(1,16299),each=2), width=1), strand=rep(c("+","-"),2), seqlengths=c(chrM=16299)) ## isCircularchrM.gr) <- TRUE ## chrM.gr ## GRanges with 4 ranges and 0 elementMetadata values: ## seqnames ranges strand ## <rle> <iranges> <rle> ## [1] chrM [ 1, 1] + ## [2] chrM [ 1, 1] - ## [3] chrM [16299, 16299] + ## [4] chrM [16299, 16299] - ## --- ## seqlengths: ## chrM ## 16299 ## seqinfochrM.gr) ## Seqinfo of length 1 ## seqnames seqlengths isCircular ## chrM 16299 TRUE ## shiftchrM.gr, shift=50) ## GRanges with 4 ranges and 0 elementMetadata values: ## seqnames ranges strand ## <rle> <iranges> <rle> ## [1] chrM [ 51, 51] + ## [2] chrM [ 51, 51] - ## [3] chrM [16299, 16299] + ## [4] chrM [16299, 16299] - ## --- ## seqlengths: ## chrM ## 16299 ## Warning message: ## In `end<-`(`*tmp*`, check = FALSE, value = c(51L, 51L, 16349L, 16349L : ## trimmed end values to be <= seqlengths ## shiftchrM.gr, shift=50 * as.integerifelsestrandchrM.gr)=="-", -1, 1))) ## Error in validObject(x) : ## invalid class “IRanges” object: 'widths(x)' cannot contain negative values ## In addition: Warning messages: ## 1: In `end<-`(`*tmp*`, check = FALSE, value = c(51L, -49L, 16349L, : ## trimmed end values to be <= seqlengths ## 2: In `start<-`(`*tmp*`, value = c(51L, -49L, 16299L, 16249L)) : ## trimmed start values to be positive ## ## ## ################################################################### ########## ## sessionInfo() ## R Under development (unstable) (2011-08-29 r56824) ## Platform: x86_64-unknown-linux-gnu (64-bit) ## locale: ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 ## [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C ## attached base packages: ## [1] stats graphics grDevices utils datasets methods base ## other attached packages: ## [1] GenomicRanges_1.5.31 IRanges_1.11.26 ## ## ################################################################### ##########
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@michael-lawrence-3846
Last seen 3.0 years ago
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As a sort of side-comment, you might be better off doing this with resize(), i.e., resize(gr, width(gr) - 50, fix = "end") Michael On Thu, Sep 1, 2011 at 5:27 AM, Ivanek, Robert <robert.ivanek@fmi.ch> wrote: > Dear Bioc developers, > > I am analysing the ChIP-Seq data using the GenomicRanges package. I am > usually shifting the reads to the middle of the fragment (i.e. by 50 bp > toward 3' end of the fragment according the strand of the read), using the > shift function (from IRanges), which works in most cases. > > shift(gr, shift=50 * as.integer(ifelse(strand(gr)==**"-", -1, 1))) > > However sometimes the result does not look like as I would expect: > > 1. If the read is on the minus strand and the start value is smaller than > the shift value, it produces an error: > > ## Error in validObject(x) : > ## invalid class “IRanges” object: 'widths(x)' cannot contain negative > values > > If the read is on the plus strand at the end of the chromosome it returns > the size of the chromosome as a new end value. Would be possible to apply > similar strategy for the beginning of the chromosome (It would return 1 as a > start value)? > > > > 2. The shift function does not take into account information about > circularity of the chromosome. Is there any plan to include it? > > > Please see below reproducible examples > > Best Regards > > Robert > > -- > Robert Ivanek > Postdoctoral Fellow Schuebeler Group > Friedrich Miescher Institute > Maulbeerstrasse 66 > 4058 Basel / Switzerland > Office phone: +41 61 697 6100 > > > > > EXAMPLES: > > > ## ##############################**##############################** > ################# > ## > library("GenomicRanges") > ## Loading required package: IRanges > ## Attaching package: ‘IRanges’ > ## The following object(s) are masked from ‘package:base’: > ## cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, > pmin, pmin.int, rbind, rep.int, setdiff, table, union > > ## > ## ##############################**##############################** > ################# > ## > chr1.gr <- GRanges(seqnames=Rle("chr1", 4), > ranges=IRanges(start=rep(c(1,**197195432),each=2), width=1), > strand=rep(c("+","-"),2), > seqlengths=c(chr1=197195432)) > ## > > isCircularchr1.gr) <- FALSE > ## > > chr1.gr > ## GRanges with 4 ranges and 0 elementMetadata values: > ## seqnames ranges strand > ## <rle> <iranges> <rle> > ## [1] chr1 [ 1, 1] + > ## [2] chr1 [ 1, 1] - > ## [3] chr1 [197195432, 197195432] + > ## [4] chr1 [197195432, 197195432] - > ## --- > ## seqlengths: > ## chr1 > ## 197195432 > ## > > seqinfochr1.gr) > ## Seqinfo of length 1 > ## seqnames seqlengths isCircular > ## chr1 197195432 FALSE > ## > > shiftchr1.gr, shift=50) > ## GRanges with 4 ranges and 0 elementMetadata values: > ## seqnames ranges strand > ## <rle> <iranges> <rle> > ## [1] chr1 [ 51, 51] + > ## [2] chr1 [ 51, 51] - > ## [3] chr1 [197195432, 197195432] + > ## [4] chr1 [197195432, 197195432] - > ## --- > ## seqlengths: > ## chr1 > ## 197195432 > ## Warning message: > ## In `end<-`(`*tmp*`, check = FALSE, value = c(51L, 51L, 197195482L, : > ## trimmed end values to be <= seqlengths > ## > > shiftchr1.gr, shift=50 * as.integer(ifelse(strand(chr1.**gr<http: chr1.gr="">)=="-", > -1, 1))) > ## Error in validObject(x) : > ## invalid class “IRanges” object: 'widths(x)' cannot contain negative > values > ## In addition: Warning messages: > ## 1: In `end<-`(`*tmp*`, check = FALSE, value = c(51L, -49L, 197195482L, > : > ## trimmed end values to be <= seqlengths > ## 2: In `start<-`(`*tmp*`, value = c(51L, -49L, 197195432L, 197195382L : > ## trimmed start values to be positive > ## > ## ##############################**##############################** > ################# > ## > chrM.gr <- GRanges(seqnames=Rle("chrM", 4), > ranges=IRanges(start=rep(c(1,**16299),each=2), width=1), > strand=rep(c("+","-"),2), > seqlengths=c(chrM=16299)) > ## > > isCircularchrM.gr) <- TRUE > ## > > chrM.gr > ## GRanges with 4 ranges and 0 elementMetadata values: > ## seqnames ranges strand > ## <rle> <iranges> <rle> > ## [1] chrM [ 1, 1] + > ## [2] chrM [ 1, 1] - > ## [3] chrM [16299, 16299] + > ## [4] chrM [16299, 16299] - > ## --- > ## seqlengths: > ## chrM > ## 16299 > ## > > seqinfochrM.gr) > ## Seqinfo of length 1 > ## seqnames seqlengths isCircular > ## chrM 16299 TRUE > ## > > shiftchrM.gr, shift=50) > ## GRanges with 4 ranges and 0 elementMetadata values: > ## seqnames ranges strand > ## <rle> <iranges> <rle> > ## [1] chrM [ 51, 51] + > ## [2] chrM [ 51, 51] - > ## [3] chrM [16299, 16299] + > ## [4] chrM [16299, 16299] - > ## --- > ## seqlengths: > ## chrM > ## 16299 > ## Warning message: > ## In `end<-`(`*tmp*`, check = FALSE, value = c(51L, 51L, 16349L, 16349L : > ## trimmed end values to be <= seqlengths > ## > > shiftchrM.gr, shift=50 * as.integer(ifelse(strand(chrM.**gr)=="-", -1, > 1))) > ## Error in validObject(x) : > ## invalid class “IRanges” object: 'widths(x)' cannot contain negative > values > ## In addition: Warning messages: > ## 1: In `end<-`(`*tmp*`, check = FALSE, value = c(51L, -49L, 16349L, : > ## trimmed end values to be <= seqlengths > ## 2: In `start<-`(`*tmp*`, value = c(51L, -49L, 16299L, 16249L)) : > ## trimmed start values to be positive > ## > ## > ## ##############################**##############################** > ################# > ## > sessionInfo() > ## R Under development (unstable) (2011-08-29 r56824) > ## Platform: x86_64-unknown-linux-gnu (64-bit) > > ## locale: > ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 > LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 > ## [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C > LC_ADDRESS=C LC_TELEPHONE=C > ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > ## attached base packages: > ## [1] stats graphics grDevices utils datasets methods base > > ## other attached packages: > ## [1] GenomicRanges_1.5.31 IRanges_1.11.26 > ## > ## ##############################**##############################** > ################# > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Nevermind, I misunderstood what you were trying to do. On Thu, Sep 1, 2011 at 6:36 AM, Michael Lawrence <michafla@gene.com> wrote: > As a sort of side-comment, you might be better off doing this with > resize(), i.e., > > resize(gr, width(gr) - 50, fix = "end") > > Michael > > On Thu, Sep 1, 2011 at 5:27 AM, Ivanek, Robert <robert.ivanek@fmi.ch>wrote: > >> Dear Bioc developers, >> >> I am analysing the ChIP-Seq data using the GenomicRanges package. I am >> usually shifting the reads to the middle of the fragment (i.e. by 50 bp >> toward 3' end of the fragment according the strand of the read), using the >> shift function (from IRanges), which works in most cases. >> >> shift(gr, shift=50 * as.integer(ifelse(strand(gr)==**"-", -1, 1))) >> >> However sometimes the result does not look like as I would expect: >> >> 1. If the read is on the minus strand and the start value is smaller than >> the shift value, it produces an error: >> >> ## Error in validObject(x) : >> ## invalid class “IRanges” object: 'widths(x)' cannot contain negative >> values >> >> If the read is on the plus strand at the end of the chromosome it returns >> the size of the chromosome as a new end value. Would be possible to apply >> similar strategy for the beginning of the chromosome (It would return 1 as a >> start value)? >> >> >> >> 2. The shift function does not take into account information about >> circularity of the chromosome. Is there any plan to include it? >> >> >> Please see below reproducible examples >> >> Best Regards >> >> Robert >> >> -- >> Robert Ivanek >> Postdoctoral Fellow Schuebeler Group >> Friedrich Miescher Institute >> Maulbeerstrasse 66 >> 4058 Basel / Switzerland >> Office phone: +41 61 697 6100 >> >> >> >> >> EXAMPLES: >> >> >> ## ##############################**##############################** >> ################# >> ## >> library("GenomicRanges") >> ## Loading required package: IRanges >> ## Attaching package: ‘IRanges’ >> ## The following object(s) are masked from ‘package:base’: >> ## cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, >> pmin, pmin.int, rbind, rep.int, setdiff, table, union >> >> ## >> ## ##############################**##############################** >> ################# >> ## >> chr1.gr <- GRanges(seqnames=Rle("chr1", 4), >> ranges=IRanges(start=rep(c(1,**197195432),each=2), width=1), >> strand=rep(c("+","-"),2), >> seqlengths=c(chr1=197195432)) >> ## >> >> isCircularchr1.gr) <- FALSE >> ## >> >> chr1.gr >> ## GRanges with 4 ranges and 0 elementMetadata values: >> ## seqnames ranges strand >> ## <rle> <iranges> <rle> >> ## [1] chr1 [ 1, 1] + >> ## [2] chr1 [ 1, 1] - >> ## [3] chr1 [197195432, 197195432] + >> ## [4] chr1 [197195432, 197195432] - >> ## --- >> ## seqlengths: >> ## chr1 >> ## 197195432 >> ## >> >> seqinfochr1.gr) >> ## Seqinfo of length 1 >> ## seqnames seqlengths isCircular >> ## chr1 197195432 FALSE >> ## >> >> shiftchr1.gr, shift=50) >> ## GRanges with 4 ranges and 0 elementMetadata values: >> ## seqnames ranges strand >> ## <rle> <iranges> <rle> >> ## [1] chr1 [ 51, 51] + >> ## [2] chr1 [ 51, 51] - >> ## [3] chr1 [197195432, 197195432] + >> ## [4] chr1 [197195432, 197195432] - >> ## --- >> ## seqlengths: >> ## chr1 >> ## 197195432 >> ## Warning message: >> ## In `end<-`(`*tmp*`, check = FALSE, value = c(51L, 51L, 197195482L, : >> ## trimmed end values to be <= seqlengths >> ## >> >> shiftchr1.gr, shift=50 * as.integer(ifelse(strand(chr1.**gr<http: chr1.gr="">)=="-", >> -1, 1))) >> ## Error in validObject(x) : >> ## invalid class “IRanges” object: 'widths(x)' cannot contain negative >> values >> ## In addition: Warning messages: >> ## 1: In `end<-`(`*tmp*`, check = FALSE, value = c(51L, -49L, 197195482L, >> : >> ## trimmed end values to be <= seqlengths >> ## 2: In `start<-`(`*tmp*`, value = c(51L, -49L, 197195432L, 197195382L : >> ## trimmed start values to be positive >> ## >> ## ##############################**##############################** >> ################# >> ## >> chrM.gr <- GRanges(seqnames=Rle("chrM", 4), >> ranges=IRanges(start=rep(c(1,**16299),each=2), width=1), >> strand=rep(c("+","-"),2), >> seqlengths=c(chrM=16299)) >> ## >> >> isCircularchrM.gr) <- TRUE >> ## >> >> chrM.gr >> ## GRanges with 4 ranges and 0 elementMetadata values: >> ## seqnames ranges strand >> ## <rle> <iranges> <rle> >> ## [1] chrM [ 1, 1] + >> ## [2] chrM [ 1, 1] - >> ## [3] chrM [16299, 16299] + >> ## [4] chrM [16299, 16299] - >> ## --- >> ## seqlengths: >> ## chrM >> ## 16299 >> ## >> >> seqinfochrM.gr) >> ## Seqinfo of length 1 >> ## seqnames seqlengths isCircular >> ## chrM 16299 TRUE >> ## >> >> shiftchrM.gr, shift=50) >> ## GRanges with 4 ranges and 0 elementMetadata values: >> ## seqnames ranges strand >> ## <rle> <iranges> <rle> >> ## [1] chrM [ 51, 51] + >> ## [2] chrM [ 51, 51] - >> ## [3] chrM [16299, 16299] + >> ## [4] chrM [16299, 16299] - >> ## --- >> ## seqlengths: >> ## chrM >> ## 16299 >> ## Warning message: >> ## In `end<-`(`*tmp*`, check = FALSE, value = c(51L, 51L, 16349L, 16349L : >> ## trimmed end values to be <= seqlengths >> ## >> >> shiftchrM.gr, shift=50 * as.integer(ifelse(strand(chrM.**gr)=="-", -1, >> 1))) >> ## Error in validObject(x) : >> ## invalid class “IRanges” object: 'widths(x)' cannot contain negative >> values >> ## In addition: Warning messages: >> ## 1: In `end<-`(`*tmp*`, check = FALSE, value = c(51L, -49L, 16349L, : >> ## trimmed end values to be <= seqlengths >> ## 2: In `start<-`(`*tmp*`, value = c(51L, -49L, 16299L, 16249L)) : >> ## trimmed start values to be positive >> ## >> ## >> ## ##############################**##############################** >> ################# >> ## >> sessionInfo() >> ## R Under development (unstable) (2011-08-29 r56824) >> ## Platform: x86_64-unknown-linux-gnu (64-bit) >> >> ## locale: >> ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 >> LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 >> ## [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C >> LC_ADDRESS=C LC_TELEPHONE=C >> ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> ## attached base packages: >> ## [1] stats graphics grDevices utils datasets methods base >> >> ## other attached packages: >> ## [1] GenomicRanges_1.5.31 IRanges_1.11.26 >> ## >> ## ##############################**##############################** >> ################# >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
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Hi Michael, is there any plan to fixed these issues? Best Regards Robert On 09/01/2011 03:37 PM, Michael Lawrence wrote: > Nevermind, I misunderstood what you were trying to do. > > On Thu, Sep 1, 2011 at 6:36 AM, Michael Lawrence <michafla at="" gene.com=""> <mailto:michafla at="" gene.com="">> wrote: > > As a sort of side-comment, you might be better off doing this with > resize(), i.e., > > resize(gr, width(gr) - 50, fix = "end") > > Michael > > On Thu, Sep 1, 2011 at 5:27 AM, Ivanek, Robert <robert.ivanek at="" fmi.ch=""> <mailto:robert.ivanek at="" fmi.ch="">> wrote: > > Dear Bioc developers, > > I am analysing the ChIP-Seq data using the GenomicRanges > package. I am usually shifting the reads to the middle of the > fragment (i.e. by 50 bp toward 3' end of the fragment according > the strand of the read), using the shift function (from > IRanges), which works in most cases. > > shift(gr, shift=50 * as.integer(ifelse(strand(gr)==__"-", -1, 1))) > > However sometimes the result does not look like as I would expect: > > 1. If the read is on the minus strand and the start value is > smaller than the shift value, it produces an error: > > ## Error in validObject(x) : > ## invalid class ?IRanges? object: 'widths(x)' cannot contain > negative values > > If the read is on the plus strand at the end of the chromosome > it returns the size of the chromosome as a new end value. Would > be possible to apply similar strategy for the beginning of the > chromosome (It would return 1 as a start value)? > > > > 2. The shift function does not take into account information > about circularity of the chromosome. Is there any plan to > include it? > > > Please see below reproducible examples > > Best Regards > > Robert > > -- > Robert Ivanek > Postdoctoral Fellow Schuebeler Group > Friedrich Miescher Institute > Maulbeerstrasse 66 > 4058 Basel / Switzerland > Office phone: +41 61 697 6100 <tel:%2b41%2061%20697%206100> > > > > > EXAMPLES: > > > ## > ##############################__############################ ##__################# > ## > library("GenomicRanges") > ## Loading required package: IRanges > ## Attaching package: ?IRanges? > ## The following object(s) are masked from ?package:base?: > ## cbind, eval, intersect, Map, mapply, order, paste, pmax, > pmax.int <http: pmax.int="">, pmin, pmin.int <http: pmin.int="">, > rbind, rep.int <http: rep.int="">, setdiff, table, union > > ## > ## > ##############################__############################ ##__################# > ## > chr1.gr <http: chr1.gr=""> <- GRanges(seqnames=Rle("chr1", 4), > ranges=IRanges(start=rep(c(1,__197195432),each=2), width=1), > strand=rep(c("+","-"),2), > seqlengths=c(chr1=197195432)) > ## > > isCircularchr1.gr <http: chr1.gr="">) <- FALSE > ## > > chr1.gr <http: chr1.gr=""> > ## GRanges with 4 ranges and 0 elementMetadata values: > ## seqnames ranges strand > ## <rle> <iranges> <rle> > ## [1] chr1 [ 1, 1] + > ## [2] chr1 [ 1, 1] - > ## [3] chr1 [197195432, 197195432] + > ## [4] chr1 [197195432, 197195432] - > ## --- > ## seqlengths: > ## chr1 > ## 197195432 > ## > > seqinfochr1.gr <http: chr1.gr="">) > ## Seqinfo of length 1 > ## seqnames seqlengths isCircular > ## chr1 197195432 FALSE > ## > > shiftchr1.gr <http: chr1.gr="">, shift=50) > ## GRanges with 4 ranges and 0 elementMetadata values: > ## seqnames ranges strand > ## <rle> <iranges> <rle> > ## [1] chr1 [ 51, 51] + > ## [2] chr1 [ 51, 51] - > ## [3] chr1 [197195432, 197195432] + > ## [4] chr1 [197195432, 197195432] - > ## --- > ## seqlengths: > ## chr1 > ## 197195432 > ## Warning message: > ## In `end<-`(`*tmp*`, check = FALSE, value = c(51L, 51L, > 197195482L, : > ## trimmed end values to be <= seqlengths > ## > > shiftchr1.gr <http: chr1.gr="">, shift=50 * > as.integer(ifelse(strand(chr1.__gr <http: chr1.gr="">)=="-", -1, 1))) > ## Error in validObject(x) : > ## invalid class ?IRanges? object: 'widths(x)' cannot contain > negative values > ## In addition: Warning messages: > ## 1: In `end<-`(`*tmp*`, check = FALSE, value = c(51L, -49L, > 197195482L, : > ## trimmed end values to be <= seqlengths > ## 2: In `start<-`(`*tmp*`, value = c(51L, -49L, 197195432L, > 197195382L : > ## trimmed start values to be positive > ## > ## > ##############################__############################ ##__################# > ## > chrM.gr <- GRanges(seqnames=Rle("chrM", 4), > ranges=IRanges(start=rep(c(1,__16299),each=2), width=1), > strand=rep(c("+","-"),2), > seqlengths=c(chrM=16299)) > ## > > isCircularchrM.gr) <- TRUE > ## > > chrM.gr > ## GRanges with 4 ranges and 0 elementMetadata values: > ## seqnames ranges strand > ## <rle> <iranges> <rle> > ## [1] chrM [ 1, 1] + > ## [2] chrM [ 1, 1] - > ## [3] chrM [16299, 16299] + > ## [4] chrM [16299, 16299] - > ## --- > ## seqlengths: > ## chrM > ## 16299 > ## > > seqinfochrM.gr) > ## Seqinfo of length 1 > ## seqnames seqlengths isCircular > ## chrM 16299 TRUE > ## > > shiftchrM.gr, shift=50) > ## GRanges with 4 ranges and 0 elementMetadata values: > ## seqnames ranges strand > ## <rle> <iranges> <rle> > ## [1] chrM [ 51, 51] + > ## [2] chrM [ 51, 51] - > ## [3] chrM [16299, 16299] + > ## [4] chrM [16299, 16299] - > ## --- > ## seqlengths: > ## chrM > ## 16299 > ## Warning message: > ## In `end<-`(`*tmp*`, check = FALSE, value = c(51L, 51L, > 16349L, 16349L : > ## trimmed end values to be <= seqlengths > ## > > shiftchrM.gr, shift=50 * > as.integer(ifelse(strand(chrM.__gr)=="-", -1, 1))) > ## Error in validObject(x) : > ## invalid class ?IRanges? object: 'widths(x)' cannot contain > negative values > ## In addition: Warning messages: > ## 1: In `end<-`(`*tmp*`, check = FALSE, value = c(51L, -49L, > 16349L, : > ## trimmed end values to be <= seqlengths > ## 2: In `start<-`(`*tmp*`, value = c(51L, -49L, 16299L, 16249L)) : > ## trimmed start values to be positive > ## > ## > ## > ##############################__############################ ##__################# > ## > sessionInfo() > ## R Under development (unstable) (2011-08-29 r56824) > ## Platform: x86_64-unknown-linux-gnu (64-bit) > > ## locale: > ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 > LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 > ## [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C > LC_TELEPHONE=C > ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > ## attached base packages: > ## [1] stats graphics grDevices utils datasets methods base > > ## other attached packages: > ## [1] GenomicRanges_1.5.31 IRanges_1.11.26 > ## > ## > ##############################__############################ ##__################# > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- Robert Ivanek Postdoctoral Fellow Schuebeler Group Friedrich Miescher Institute Maulbeerstrasse 66 4058 Basel / Switzerland Office phone: +41 61 697 6100
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Yes. I am guessing that Herve is going to pick this one up. Michael On Thu, Sep 1, 2011 at 8:23 AM, Ivanek, Robert <robert.ivanek@fmi.ch> wrote: > Hi Michael, > > is there any plan to fixed these issues? > > Best Regards > > Robert > > > On 09/01/2011 03:37 PM, Michael Lawrence wrote: > >> Nevermind, I misunderstood what you were trying to do. >> >> On Thu, Sep 1, 2011 at 6:36 AM, Michael Lawrence <michafla@gene.com>> <mailto:michafla@gene.com>> wrote: >> >> As a sort of side-comment, you might be better off doing this with >> resize(), i.e., >> >> resize(gr, width(gr) - 50, fix = "end") >> >> Michael >> >> On Thu, Sep 1, 2011 at 5:27 AM, Ivanek, Robert <robert.ivanek@fmi.ch>> <mailto:robert.ivanek@fmi.ch>> wrote: >> >> Dear Bioc developers, >> >> I am analysing the ChIP-Seq data using the GenomicRanges >> package. I am usually shifting the reads to the middle of the >> fragment (i.e. by 50 bp toward 3' end of the fragment according >> the strand of the read), using the shift function (from >> IRanges), which works in most cases. >> >> shift(gr, shift=50 * as.integer(ifelse(strand(gr)==**__"-", -1, >> 1))) >> >> However sometimes the result does not look like as I would expect: >> >> 1. If the read is on the minus strand and the start value is >> smaller than the shift value, it produces an error: >> >> ## Error in validObject(x) : >> ## invalid class “IRanges” object: 'widths(x)' cannot contain >> negative values >> >> If the read is on the plus strand at the end of the chromosome >> it returns the size of the chromosome as a new end value. Would >> be possible to apply similar strategy for the beginning of the >> chromosome (It would return 1 as a start value)? >> >> >> >> 2. The shift function does not take into account information >> about circularity of the chromosome. Is there any plan to >> include it? >> >> >> Please see below reproducible examples >> >> Best Regards >> >> Robert >> >> -- >> Robert Ivanek >> Postdoctoral Fellow Schuebeler Group >> Friedrich Miescher Institute >> Maulbeerstrasse 66 >> 4058 Basel / Switzerland >> Office phone: +41 61 697 6100 <tel:%2b41%2061%20697%206100> >> >> >> >> >> >> EXAMPLES: >> >> >> ## >> ##############################**__############################** >> ##__################# >> ## >> library("GenomicRanges") >> ## Loading required package: IRanges >> ## Attaching package: ‘IRanges’ >> ## The following object(s) are masked from ‘package:base’: >> ## cbind, eval, intersect, Map, mapply, order, paste, pmax, >> pmax.int <http: pmax.int="">, pmin, pmin.int <http: pmin.int="">, >> rbind, rep.int <http: rep.int="">, setdiff, table, union >> >> ## >> ## >> ##############################**__############################** >> ##__################# >> ## >> chr1.gr <http: chr1.gr=""> <- GRanges(seqnames=Rle("chr1", 4), >> >> ranges=IRanges(start=rep(c(1,_**_197195432),each=2), width=1), >> strand=rep(c("+","-"),2), >> seqlengths=c(chr1=197195432)) >> ## >> >> isCircularchr1.gr <http: chr1.gr="">) <- FALSE >> ## >> >> chr1.gr <http: chr1.gr=""> >> >> ## GRanges with 4 ranges and 0 elementMetadata values: >> ## seqnames ranges strand >> ## <rle> <iranges> <rle> >> ## [1] chr1 [ 1, 1] + >> ## [2] chr1 [ 1, 1] - >> ## [3] chr1 [197195432, 197195432] + >> ## [4] chr1 [197195432, 197195432] - >> ## --- >> ## seqlengths: >> ## chr1 >> ## 197195432 >> ## >> >> seqinfochr1.gr <http: chr1.gr="">) >> >> ## Seqinfo of length 1 >> ## seqnames seqlengths isCircular >> ## chr1 197195432 FALSE >> ## >> >> shiftchr1.gr <http: chr1.gr="">, shift=50) >> >> ## GRanges with 4 ranges and 0 elementMetadata values: >> ## seqnames ranges strand >> ## <rle> <iranges> <rle> >> ## [1] chr1 [ 51, 51] + >> ## [2] chr1 [ 51, 51] - >> ## [3] chr1 [197195432, 197195432] + >> ## [4] chr1 [197195432, 197195432] - >> ## --- >> ## seqlengths: >> ## chr1 >> ## 197195432 >> ## Warning message: >> ## In `end<-`(`*tmp*`, check = FALSE, value = c(51L, 51L, >> 197195482L, : >> ## trimmed end values to be <= seqlengths >> ## >> >> shiftchr1.gr <http: chr1.gr="">, shift=50 * >> as.integer(ifelse(strand(chr1.**__gr <http: chr1.gr="">)=="-", -1, >> 1))) >> >> ## Error in validObject(x) : >> ## invalid class “IRanges” object: 'widths(x)' cannot contain >> negative values >> ## In addition: Warning messages: >> ## 1: In `end<-`(`*tmp*`, check = FALSE, value = c(51L, -49L, >> 197195482L, : >> ## trimmed end values to be <= seqlengths >> ## 2: In `start<-`(`*tmp*`, value = c(51L, -49L, 197195432L, >> 197195382L : >> ## trimmed start values to be positive >> ## >> ## >> ##############################**__############################** >> ##__################# >> ## >> chrM.gr <- GRanges(seqnames=Rle("chrM", 4), >> ranges=IRanges(start=rep(c(1,_**_16299),each=2), width=1), >> strand=rep(c("+","-"),2), >> seqlengths=c(chrM=16299)) >> ## >> >> isCircularchrM.gr) <- TRUE >> ## >> >> chrM.gr >> ## GRanges with 4 ranges and 0 elementMetadata values: >> ## seqnames ranges strand >> ## <rle> <iranges> <rle> >> ## [1] chrM [ 1, 1] + >> ## [2] chrM [ 1, 1] - >> ## [3] chrM [16299, 16299] + >> ## [4] chrM [16299, 16299] - >> ## --- >> ## seqlengths: >> ## chrM >> ## 16299 >> ## >> >> seqinfochrM.gr) >> ## Seqinfo of length 1 >> ## seqnames seqlengths isCircular >> ## chrM 16299 TRUE >> ## >> >> shiftchrM.gr, shift=50) >> ## GRanges with 4 ranges and 0 elementMetadata values: >> ## seqnames ranges strand >> ## <rle> <iranges> <rle> >> ## [1] chrM [ 51, 51] + >> ## [2] chrM [ 51, 51] - >> ## [3] chrM [16299, 16299] + >> ## [4] chrM [16299, 16299] - >> ## --- >> ## seqlengths: >> ## chrM >> ## 16299 >> ## Warning message: >> ## In `end<-`(`*tmp*`, check = FALSE, value = c(51L, 51L, >> 16349L, 16349L : >> ## trimmed end values to be <= seqlengths >> ## >> >> shiftchrM.gr, shift=50 * >> as.integer(ifelse(strand(chrM.**__gr)=="-", -1, 1))) >> ## Error in validObject(x) : >> ## invalid class “IRanges” object: 'widths(x)' cannot contain >> negative values >> ## In addition: Warning messages: >> ## 1: In `end<-`(`*tmp*`, check = FALSE, value = c(51L, -49L, >> 16349L, : >> ## trimmed end values to be <= seqlengths >> ## 2: In `start<-`(`*tmp*`, value = c(51L, -49L, 16299L, 16249L)) : >> ## trimmed start values to be positive >> ## >> ## >> ## >> ##############################**__############################** >> ##__################# >> ## >> sessionInfo() >> ## R Under development (unstable) (2011-08-29 r56824) >> ## Platform: x86_64-unknown-linux-gnu (64-bit) >> >> ## locale: >> ## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 >> LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 >> ## [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C >> LC_TELEPHONE=C >> ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> ## attached base packages: >> ## [1] stats graphics grDevices utils datasets methods base >> >> ## other attached packages: >> ## [1] GenomicRanges_1.5.31 IRanges_1.11.26 >> ## >> ## >> ##############################**__############################** >> ##__################# >> >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.**science.biology.informatics.** >> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> >> >> >> > -- > Robert Ivanek > Postdoctoral Fellow Schuebeler Group > Friedrich Miescher Institute > Maulbeerstrasse 66 > 4058 Basel / Switzerland > Office phone: +41 61 697 6100 > [[alternative HTML version deleted]]
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