[Bioc-sig-seq] Error message when working with IRanges package

[pterry at huskers.unl.edu]

Dear bioc-sig-sequencing,

Can you comment on the following error message I received while using the IRanges package.

I tried the following with a gene information file downloaded from UCSC Table Browser (C. elegans, chrIII):

The first two lines of the gene information file are:

mterry at system76-pc:~/data09/R_working$ head -n 2 celegans_chrIII.txt
#name   chrom   strand  txStart txEnd   cdsStart        cdsEnd  exonCount       exonStarts      exonEnds        proteinID
cTel54X.1       chrIII  -       1270    2917    1270    2917    4       1270,1557,2680,2816,    1507,2167,2764,2917,    fbxa-6

genetable<-read.table("celegans_chrIII.txt", header=T, sep="\t")
> head(genetable, n = 2L)
  cTel54X.1 chrIII X. X1270 X2917 X1270.1 X2917.1 X4
1  H10E21.2 chrIII  +  8855 11940    8855   11940  6
2 H10E21.3a chrIII  - 12185 14801   12188   14753  7
                       X1270.1557.2680.2816.
1          8855,9268,9886,10515,10796,11674,
2 12185,12475,12964,13463,13811,14521,14740,
                       X1507.2167.2764.2917.   fbxa.6
1         8957,9428,10072,10641,11105,11940, H10E21.2
2 12401,12627,13391,13682,14083,14686,14801,   nhr-80
>

##############################################################
I note: the preceding 'read.table' command made the 1st data line in 'genetable' into sort of a header?  The error in the following code line cites a problem in row 1 of the 'genetable' data structure.
################################################################

> promoter<-IRanges(start=genetable$txStart-1000*as.real(genetable$strand=="+"), width=1000)
Error in solveUserSEW0(start = start, end = end, width = width) :
  solving row 1: range cannot be determined from the supplied arguments (too many NAs)

> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-09-11 r49665)
x86_64-unknown-linux-gnu

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=C              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] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ShortRead_1.3.40   lattice_0.17-26    rtracklayer_1.5.23 RCurl_1.2-1
[5] bitops_1.0-4.1     BSgenome_1.13.16   Biostrings_2.13.52 IRanges_1.3.93

loaded via a namespace (and not attached):
[1] Biobase_2.5.8 grid_2.10.0   hwriter_1.1   XML_2.6-0
>

Thanks,
P. Terry
pterry at huskers.unl.edu