Entering edit mode
Tim Smith
★
1.1k
@tim-smith-1532
Last seen 10.2 years ago
Hi,
I was just trying out the rtracklayer package with the example given
in the
bioinformatics paper on rtracklayer. Here is my code and the error
statement:
> library(IRanges)
> library(rtracklayer)
> data(targets)
> tt <-
>with(targets,GenomicData(IRanges(start,end),target,strand=strand,chro
m=chrom))
> class(tt)
[1] "RangedData"
attr(,"package")
[1] "IRanges"
> session <- browserSession()
> session$targets <- tt
Error in FUN(X[[1L]], ...) :
Invalid chromosomes for hg19: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14,
15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT
My sessionInfo and traceback for the error are:
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets
methods
base
other attached packages:
[1] hash_2.1.0 biomaRt_2.8.0 rtracklayer_1.12.2
RCurl_1.5-0
bitops_1.0-4.1
[6] IRanges_1.10.4 pvclust_1.2-2 les_1.2.0
fdrtool_1.2.7
ggplot2_0.8.9
[11] proto_0.3-9.2 reshape_0.8.4 plyr_1.5.2
loaded via a namespace (and not attached):
[1] Biostrings_2.20.1 boot_1.2-43 BSgenome_1.20.0
gdata_2.8.1 GenomicRanges_1.4.6
[6] gplots_2.8.0 gtools_2.6.2 RColorBrewer_1.0-2
tools_2.13.0 XML_3.4-0
> traceback()
15: stop("Invalid chromosomes for ", genome(session), ": ",
paste(badSpaces,
collapse = ", "))
14: FUN(X[[1L]], ...)
13: lapply(split(X, group), FUN, ...)
12: tapply(value, unlist(genomes), function(tracks) {
genome <- genome(tracks[[1]])
if (length(genome))
genome(session) <- genome
spaces <- unlist(lapply(tracks, names))
badSpaces <- setdiff(spaces, seqnames(session))
if (length(badSpaces))
stop("Invalid chromosomes for ", genome(session), ": ",
paste(badSpaces, collapse = ", "))
})
11: normArgTrackData(value, session)
10: .local(object, ..., value = value)
9: `track<-`(`*tmp*`, name, ..., value = <s4 object="" of="" class="" "rangeddatalist"="">)
8: `track<-`(`*tmp*`, name, ..., value = <s4 object="" of="" class="" "rangeddatalist"="">)
7: .local(object, ..., value = value)
6: `track<-`(`*tmp*`, i, ..., value = <s4 object="" of="" class="" "rangeddata"="">)
5: `track<-`(`*tmp*`, i, ..., value = <s4 object="" of="" class="" "rangeddata"="">)
4: `[[<-`(`*tmp*`, name, value = <s4 object="" of="" class="" "rangeddata"="">)
3: `[[<-`(`*tmp*`, name, value = <s4 object="" of="" class="" "rangeddata"="">)
2: `$<-`(`*tmp*`, "targets", value = <s4 object="" of="" class="" "rangeddata"="">)
1: `$<-`(`*tmp*`, "targets", value = <s4 object="" of="" class="" "rangeddata"="">)
[[alternative HTML version deleted]]
