[BioC] Error in solveUserSEW0 when using get.targets in TEQC

[Johanna Hasmats]

Dear all,

I am trying to load the exome bed file "2.1M_Human_Exome.bed" provided by
NimbleGen
(http://www.nimblegen.com/downloads/annotation/seqcap_exome/2.1M_Human_Exome
_Annotation.zip) as a target by using get.targets in the TEQC package.

However, I get this error message:

Error in solveUserSEW0(start = start, end = end, width = width) : 
  solving row 175279: range cannot be determined from the supplied arguments
(too many NAs)

and I cannot seem to come around it. Tried if conditions as well as
na.omit/exclude but without results.

> traceback()
4: .Call("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
3: solveUserSEW0(start = start, end = end, width = width)
2: IRanges(start = dat[, startcol], end = dat[, endcol])
1: get.targets("2.1M_Human_Exome.bed", chrcol = 1, startcol = 2, 
       endcol = 3)

> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] TEQC_0.99.2   IRanges_1.8.9

loaded via a namespace (and not attached):
[1] Biobase_2.10.0 tools_2.12.2  

Could somebody help me out with this? 

Thanks in advance,

Johanna


############################################################
Kindly
 
Johanna Hasmats, M.Sc, PhD Student
Division of Gene Technology, School of Biotechnology, KTH
SciLifeLab
Phone: +46(0)73 625 14 60
 
Postal address:
Box 1031
171 21 Solna
 
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