hey, speaking of which -- I always have to convert vstep WIG files to
bedGraph (e.g. for Cui & Zhao's CD133/CD36 ChIPseq results) in order to
import them.

Is that pretty much the norm or is something wrong?  I've tried renaming
them, etc. but conversion to bedGraph gives me better results.

Also, I wrote a function to directly import MACS output, does anyone want
it in rtracklayer?



On Fri, Mar 23, 2012 at 10:20 AM, Michael Lawrence <
lawrence.michael@gene.com> wrote:

> On Fri, Mar 23, 2012 at 8:59 AM, Vincent Schulz <Vincent.Schulz@yale.edu
> >wrote:
>
> > Hi,
> >
> > I can no longer generate variableStep wig files in R2.14 (or 2.13 or
> 2.12)
> > but it works in 2.11. Example below:
> >
> > library(IRanges)
> > library(rtracklayer)
> > dummy <- file() # dummy file connection for demo
> > track2 <- RangedData(IRanges(start = c(1, 72, 74, 76, 77,
> 94,108,151,152),
> > end = c(71,  73,  75,  76,  93, 107, 150, 151, 152)),
> > score = c(3,4,5,8,9,10,11,14,15),
> > space = c("chr1", "chr1", "chr1", "chr1", "chr1",
> > "chr1","chr1","chr1","chr1"))
> > wig <- export.wig(track2, dummy, dataFormat = "variableStep")
> >
> > Error in FUN(X[i], ...) :
> >  The span must be uniform for Wiggle export. Consider bedGraph or bigWig
> > as alternatives.
> >
> > Note that is does work if the regions are all of the same size, but then
> > what is the point of variableStep?  Could this possibly be fixed in R2.15
> > (if it isn't already)?
> >
> >
> The variableStep format means that the separation of intervals is
> non-uniform. The width must be uniform. Back in R 2.11, rtracklayer was
> exporting invalid WIG files (by creating multiple blocks of different
> spans; UCSC told me this was not legal).
>
>
> > Another question, apologies that it is unrelated, probably obvious, and
> > not bioconductor specific: How do I see code for S4 functions?  What I
> > tried below is unhelpfully recursive:
> >
> > getMethod(export.ucsc)
> > Method Definition:
> >
> > function (object, con, subformat = c("auto", "gff1", "wig", "bed",
> >    "bed15", "bedGraph"), append = FALSE, ...)
> > {
> >    cl <- class(object)
> >    track <- try(as(object, "RangedData"), silent = TRUE)
> >    if (class(track) == "try-error") {
> >        track <- try(as(object, "RangedDataList"), silent = TRUE)
> >        if (class(track) == "try-error")
> >            stop("cannot export object of class '", cl, "'")
> >    }
> >    export.ucsc(track, con = con, subformat = subformat, append = append,
> >        ...)
> > }
> > <environment: namespace:rtracklayer>
> >
> > Signatures:
> >        object con
> > target  "ANY"  "ANY"
> > defined "ANY"  "ANY"
> >
> >
> See ?selectMethod.
>
>
> > Thanks,
> >
> > Vince
> >
> > sessionInfo()
> > R version 2.14.2 (2012-02-29)
> > Platform: x86_64-pc-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=C                 LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] IRanges_1.12.5     rtracklayer_1.14.4 RCurl_1.91-1
> bitops_1.0-4.1
> >
> > loaded via a namespace (and not attached):
> > [1] Biostrings_2.22.0   BSgenome_1.22.0     GenomicRanges_1.6.7
> > [4] tools_2.14.2        XML_3.9-4           zlibbioc_1.0.0
> >
> > ______________________________**_________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
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> 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>
> >
>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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