[BioC] rtracklayer 'track' method, a viewLimits parameter?

Paul Shannon pshannon at systemsbiology.org
Fri Oct 29 18:44:32 CEST 2010

Hi Michael,

In creating a minimal script to demonstrate my track<- viewLimits problem, I got past the 'unused argument' but stuck at the next step.  In other programs I have written, I do not see *this* particular problem.   Something nondeterministic seems to be going on for me.   Maybe you can see what I am doing wrong.

Here is the 14-line script.  I'll be grateful for any help you can give.

library (rtracklayer)
library (GenomicFeatures)

score <- c (80.3, 99.5)
chrom.names <- c ('chr1', 'chr1')
feature.locs <- IRanges (c (201491492, 201491528),  c (201491520, 201491607))
strand <- c ('+', '+')
name = Rle (c ('feature-1', 'feature-2'))
feature.grange <- GRangesForUCSCGenome ('hg18', chrom.names, feature.locs, strand, name, score)
view.range <- GRanges (seqnames='chr1', range=c(201491480, 20149120))   # slightly larger than the region covered by the features
session <- browserSession ('UCSC')
track.name <- 'demoFeatures'
track (session, track.name, viewLimits=c(80,100)) <- feature.grange
stopifnot (track.name %in%  names (trackNames (session)))
view <- browserView (session, view.range, full='cytoBand', dense=c ('ruler', 'chainNetPanTro2', 'chainNetMm9'), hide=trackNames (session))

---- sessionInfo

R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GenomicFeatures_1.1.11 GenomicRanges_1.2.0    IRanges_1.8.0          rtracklayer_1.10.2     RCurl_1.4-3            bitops_1.0-4.1

loaded via a namespace (and not attached):
[1] Biobase_2.10.0    biomaRt_2.6.0     Biostrings_2.18.0 BSgenome_1.17.5   DBI_0.2-5         RSQLite_0.9-2     XML_3.2-0

On Oct 28, 2010, at 4:03 PM, Michael Lawrence wrote:

> On Thu, Oct 28, 2010 at 1:21 PM, Paul Shannon <pshannon at systemsbiology.org> wrote:
> I have a specific rtracklayer question, and a general S4/help question.
> The specific question:  Michael helpfully suggested  the 'viewLimits' parameter to the rtracklayer track method, saying
>     This is another track line parameter, called viewLimits. See class?GraphTrackLine.
>     track (session, "wiggle", viewLimits = c(0, 100)) <- wiggle
> Indeed, class?GraphTrackLine mentions that parameter.
> But when I call this method (or what I *think* is this method), I get this:
>    unused argument(s) (viewLimits = c(80, 100))
> That's my specific question.   How do I supply viewLimits information to the track method?
> Could you please provide a reproducible example? I cannot reproduce with a simple test, and really the arguments are not interpreted in a way that would result in that error. 

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