Entering edit mode
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)?
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"
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
