Thanks, I figured it might just come down to updating. And yes, I did mean nonstandard columns -- even though it's not "really" a BED file, it's still helpful to be able to import just the first 3 columns so that my script can handle any type of BED-like file, standard or not. The ability to select columns will be helpful in the future, thanks. -Nathan On 08/30/2011 01:05 AM, Michael Lawrence wrote: > And also, just btw, > > What do you mean by a BED file more than three columns? rtracklayer can > read those in just fine, unless they are non-standard columns, in which > case you really don't have a BED file anyway. > > With newer versions of rtracklayer, one can specify the colnames > argument to select only the desired BED columns. Passing character() > would give you your desired result. > > Michael > > On Mon, Aug 29, 2011 at 4:02 PM, Michael Lawrence <michafla at="" gene.com=""> <mailto:michafla at="" gene.com="">> wrote: > > I can't reproduce this: > > > import(pipe("cat ~/tmp/pipe-test.bed"), format="bed") > > RangedData with 4 rows and 0 value columns across 3 spaces > space ranges | > <factor> <iranges> | > > 1 chr1 [108503809, 108508915] | > 2 chr17 [ 60212870, 60218774] | > 3 chr8 [ 86373507, 86380637] | > 4 chr8 [ 99303547, 99307608] | > > sessionInfo() > R version 2.14.0 Under development (unstable) (--) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] C > > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.13.12 RCurl_1.5-0 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] BSgenome_1.21.3 Biostrings_2.21.6 GenomicRanges_1.5.21 > [4] IRanges_1.11.16 XML_3.2-0 zlibbioc_0.1.6 > > > I don't remember this being an issue in the past, but who knows. My > only recommendation is to upgrade your R and rtracklayer. > > Michael > > > On Mon, Aug 29, 2011 at 8:56 AM, Nathan Sheffield > <nathan.sheffield at="" duke.edu="" <mailto:nathan.sheffield="" at="" duke.edu="">> wrote: > > Hi, > > I am having trouble with importing a bed file after running it > through pipe() in R. Maybe it's a bug in rtracklayer's > import.bed ? Or maybe I'm missing a setting, can anyone help > with this? > > I have a bed file ("code25.bed") with 4 lines: > chr17 60212869 60218774 > chr1 108503808 108508915 > chr8 86373506 86380637 > chr8 99303546 99307608 > > I can read it into R with read.table like so: > > read.table("Aug5/codeBed/__code25.bed") > > V1 V2 V3 > 1 chr17 60212869 60218774 > 2 chr1 108503808 108508915 > 3 chr8 86373506 86380637 > 4 chr8 99303546 99307608 > > I want to use rtracklayer to import to get a genomicRanges > object, so I try with import.bed, which also works: > > import.bed("Aug5/codeBed/__code25.bed") > > RangedData with 4 rows and 0 value columns across 3 spaces > space ranges | > <character> <iranges> | > 1 chr1 [108503809, 108508915] | > 2 chr17 [ 60212870, 60218774] | > 3 chr8 [ 86373507, 86380637] | > 4 chr8 [ 99303547, 99307608] | > > Now, I want this to work on bed files with more than 3 columns, > just in case. I can do this with a commandline pipe using cut > like so: > > read.table(pipe(paste("cut -f1,2,3 ", > "Aug5/codeBed/code25.bed"))) > > V1 V2 V3 > 1 chr17 60212869 60218774 > 2 chr1 108503808 108508915 > 3 chr8 86373506 86380637 > 4 chr8 99303546 99307608 > > So this gives the exact same output as the first read.table > above. However, when I try to pass this pipe to import.bed, > something strange happens: > > import.bed(pipe(paste("cut -f1,2,3 ", > "Aug5/codeBed/code25.bed"))) > > RangedData with 5 rows and 0 value columns across 3 spaces > space ranges | > <character> <iranges> | > 1 chr1 [108503809, 108508915] | > 2 chr17 [ 60212870, 60218774] | > 3 chr17 [ 60212870, 60218774] | > 4 chr8 [ 86373507, 86380637] | > 5 chr8 [ 99303547, 99307608] | > > Not sure why, but it has duplicated one of the regions and now > has 5, instead of 4. This is a problem with import.bed combined > with pipe, and has nothing to do with cut: > > import.bed(pipe("cat Aug5/codeBed/code25.bed")) > > RangedData with 5 rows and 0 value columns across 3 spaces > space ranges | > <character> <iranges> | > 1 chr1 [108503809, 108508915] | > 2 chr17 [ 60212870, 60218774] | > 3 chr17 [ 60212870, 60218774] | > 4 chr8 [ 86373507, 86380637] | > 5 chr8 [ 99303547, 99307608] | > > > any ideas? > > -Nathan Sheffield > Duke University, Computational Biology Program > > sessionInfo follows: > > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=no_NO.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=no_NO.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.10.6 RCurl_1.4-3 bitops_1.0-4.1 > [4] GenomicRanges_1.2.1 IRanges_1.8.7 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 Biostrings_2.18.0 BSgenome_1.18.0 XML_3.2-0 > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" 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.conductor=""> > > >