Hi, Bringing the conversation back to the list. There should be no need to lapply. psetdiff(x, y) is vectorized. It computes element-wise (parallel) asymmetric differences between 'x' and 'y'.'x' should be all gene ranges and 'y' a GRangesList (same length as 'x') containing the components of each gene. The result will be a GRangesList the same length as the number of genes. Valerie > On 09/10/2013 07:34 PM, Carl Baribault wrote:> Valerie, >> >> Thanks for your input. FYI, my bed file has only 1 preferred isoform >> per gene (subset from refSeq 05/01/2012 if I recall). I already have >> the import working, thank you. The following is just one element of >> what I want to obtain. I just need to lapply/vectorize the right way. >> Your thoughts? >> >> Best, >> Carl >> > psetdiff(range(ref1), blocks(ref1)) >> GRangesList of length 1: >> $1 >> GRanges with 2 ranges and 0 metadata columns: >> seqnames ranges strand >> <rle> <iranges> <rle> >> [1] chr1 [12228, 12612] + >> [2] chr1 [12722, 13220] + >> >> --- >> seqlengths: >> chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrX chrY >> chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 >> chr22 >> NA NA NA NA NA NA NA NA NA NA NA >> NA NA NA NA NA NA NA NA NA NA NA NA NA >> > blocks(ref1) >> GRangesList of length 1: >> $1 >> GRanges with 3 ranges and 0 metadata columns: >> seqnames ranges strand >> <rle> <iranges> <rle> >> [1] chr1 [11874, 12227] + >> [2] chr1 [12613, 12721] + >> [3] chr1 [13221, 14408] + >> >> --- >> seqlengths: >> chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrX chrY >> chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 >> chr22 >> NA NA NA NA NA NA NA NA NA NA NA >> NA NA NA NA NA NA NA NA NA NA NA NA NA >> >> > On 09/10/2013 09:31 AM, Valerie Obenchain wrote: > Hi Carl, > > You can use import() from rtracklayer to read a bed in as a GRanges. > > gr <- import('myfile.bed', asRangedData=FALSE) > > I'm not sure what you've got in your file but let's say they are gene > isoforms. Presumably there is an identifier in the file that would let > you group the ranges by gene (or whatever grouping you are after). This > will likely end up as one of the metadata columns in the GRanges after > import. Create a GRangesList by grouping the GRanges by gene. > > grl <- split(gr, bySomeFactor) > > The introns are the gaps between the ranges in each list element of the > GRangesList. To get at these we want the difference between the full > range of the gene and the multiple elements (exons or transcripts etc.) > of the gene. > > Create the gene ranges: > > geneRanges <- range(grl) > > Extract the differences: > > introns <- psetdiff(geneRanges, grl) > > > If this doesn't help, I'll need to know more detail about the data in > the isoform file. > > Valerie > > > On 09/09/2013 07:31 PM, Carl Baribault wrote: >> Dear Valerie, >> I have a bed file of specific isoforms of interest. Can you please >> suggest >> a best approach for obtaining the intron extents? Thanks. >> >> Best, >> Carl Baribault >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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