I have the necessity to filter a Bam file, keeping only reads associated to a subset of references. I wanted to do it with filterBam (Rsamtools) but I could not manage to find a way of doing it. If I use the code: filterBam("onlymapped.bam", "filtered.bam", param=ScanBamParam(which=my.rnames, what=scanBamWhat("rname"))) I get: Error in function (classes, fdef, mtable) : unable to find an inherited method for function "ScanBamParam", for signature "character" checking the help it seems to me that ScanBamParam(which=) only support GRanges, RangesList, RangedData objects. There is any other way to filter a bam file on the basis of the rname? Cheers Raffaele > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.14.4 latticeExtra_0.6-24 RColorBrewer_1.0-5 lattice_0.20-10 Rsamtools_1.8.6 [6] Biostrings_2.24.1 GenomicRanges_1.8.13 IRanges_1.14.4 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] bitops_1.0-4.1 grid_2.15.1 hwriter_1.3 stats4_2.15.1 tools_2.15.1 zlibbioc_1.2.0 > -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit MBC Centro di Biotecnologie Molecolari Via Nizza 52, Torino 10126 tel. ++39 0116706457 Fax ++39 0112366457 Mobile ++39 3333827080 email: raffaele.calogero at unito.it raffaele[dot]calogero[at]gmail[dot]com www: http://www.bioinformatica.unito.it

Hi Raffaele, To read in only specific chromosomes (rnames) you can use 'which'. This toy bam file has two 'chromosomes', seq1 and seq2. Here we specify that we want a particular range of seq1. You can also request the entire length of seq1. which <- RangesList(seq1=IRanges(0, 2000)) If you only specify 'rname' in the 'what' then only that single field that will be returned. Most likely you want several fields. See ?ScanBamParam for details. what <- c("rname", "strand", "pos", "qwidth", "seq") Create the param and read in the data. param <- ScanBamParam(which=which, what=what) bamFile <- system.file("extdata", "ex1.bam", package="Rsamtools") bam <- scanBam(bamFile, param=param) Valerie On 10/18/2012 06:57 AM, rcaloger wrote: > I have the necessity to filter a Bam file, keeping only reads > associated to a subset of references. > I wanted to do it with filterBam (Rsamtools) > but I could not manage to find a way of doing it. > If I use the code: > filterBam("onlymapped.bam", "filtered.bam", > param=ScanBamParam(which=my.rnames, what=scanBamWhat("rname"))) > I get: > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "ScanBamParam", for > signature "character" > > checking the help it seems to me that ScanBamParam(which=) only > support GRanges, RangesList, RangedData objects. > > There is any other way to filter a bam file on the basis of the rname? > Cheers > Raffaele > > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.14.4 latticeExtra_0.6-24 RColorBrewer_1.0-5 > lattice_0.20-10 Rsamtools_1.8.6 > [6] Biostrings_2.24.1 GenomicRanges_1.8.13 IRanges_1.14.4 > Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] bitops_1.0-4.1 grid_2.15.1 hwriter_1.3 stats4_2.15.1 > tools_2.15.1 zlibbioc_1.2.0 > > >