Entering edit mode
Janet Young
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740
@janet-young-2360
Last seen 4.5 years ago
Fred Hutchinson Cancer Research Center,…
Hi there,
I'd love to put in a request, if I can? Using the devel version of
tracklayer, I'd like to be able to include a trackline when I export
GRanges, and RleLists, etc. It looks like that's not implemented
right now? I know there's a manual way to do this (write a trackline
to its own file, then append the export to that file), but it'd be
really nice to have that functionality in the export function at some
point in the future.
I've included some code below to show you what I mean.
thanks very much,
Janet
------------
library(rtracklayer)
### demo test item from ?export
test_path <- system.file("tests", package = "rtracklayer")
test_bed <- file.path(test_path, "test.bed")
test <- import(test_bed, asRangedData = FALSE)
test
## demo export from ?export: I do get a trackline in this file
test_bed_out <- file.path(tempdir(), "test.bed")
export(test, test_bed_out)
## for GRanges objects there's no trackline exported by default
(that's OK):
gr <- as(test,"GRanges")
export(gr, test_bed_out)
### but it'd be really nice to be able to request a trackline
specifically - it doesn't seem to be implemented right now:
myTrackLine <- new("TrackLine", name="gr", color=col2rgb("red")[,1])
export(gr, test_bed_out, trackLine=myTrackLine)
# Error in .local(object, con, format, ...) :
# unused argument (trackLine = <s4 object="" of="" class="" "trackline"="">)
## same thing for SimpleRleList
export(coverage(gr), con=test_bed_out, format="bedGraph",
trackLine=myTrackLine)
#Error in .local(object, con, format, ...) :
# unused argument (trackLine = <s4 object="" of="" class="" "trackline"="">)
### my own examples include bed files for GRanges objects, and
bedGraph files for SimpleRleList, but I can imagine other examples
too. Would it be hard to implement trackLine option for any output
format where tracklines are acceptable?
sessionInfo()
R Under development (unstable) (2013-11-06 r64163)
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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] rtracklayer_1.23.20 GenomicRanges_1.15.42 GenomeInfoDb_0.99.26
[4] IRanges_1.21.39 BiocGenerics_0.9.3
loaded via a namespace (and not attached):
[1] BatchJobs_1.2 BBmisc_1.5
[3] BiocParallel_0.5.18 Biostrings_2.31.20
[5] bitops_1.0-6 brew_1.0-6
[7] BSgenome_1.31.12 codetools_0.2-8
[9] DBI_0.2-7 digest_0.6.4
[11] fail_1.2 foreach_1.4.1
[13] GenomicAlignments_0.99.36 iterators_1.0.6
[15] plyr_1.8.1 Rcpp_0.11.1
[17] RCurl_1.95-4.1 Rsamtools_1.15.38
[19] RSQLite_0.11.4 sendmailR_1.1-2
[21] stats4_3.1.0 stringr_0.6.2
[23] tools_3.1.0 XML_3.98-1.1
[25] XVector_0.3.7 zlibbioc_1.9.0
