[BioC] rtracklayer bed import
Christian Ruckert
cruckert at uni-muenster.de
Fri Oct 30 11:38:29 CET 2009
When trying to import the example .bed track from
http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED with the
import function from rtracklayer package I get the following error message:
> tr = import("example.bed")
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
na.strings, :
line 1 did not have 9 elements
> sessionInfo()
R version 2.10.0 RC (2009-10-18 r50160)
x86_64-pc-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rtracklayer_1.6.0 RCurl_1.3-0 bitops_1.0-4.1
loaded via a namespace (and not attached):
[1] BSgenome_1.14.0 Biobase_2.6.0 Biostrings_2.14.0 IRanges_1.4.0
[5] XML_2.6-0
example.bed:
##Example 5 from Custom Annotation Tracks User's Guide
browser position chr7:127471196-127495720
browser hide all
track name="ItemRGBDemo" description="Item RGB demonstration"
visibility=2 itemRgb="On"
chr7 127471196 127472363 Pos1 0 + 127471196 127472363 255,0,0
chr7 127472363 127473530 Pos2 0 + 127472363 127473530 255,0,0
chr7 127473530 127474697 Pos3 0 + 127473530 127474697 255,0,0
chr7 127474697 127475864 Pos4 0 + 127474697 127475864 255,0,0
chr7 127475864 127477031 Neg1 0 - 127475864 127477031 0,0,255
chr7 127477031 127478198 Neg2 0 - 127477031 127478198 0,0,255
chr7 127478198 127479365 Neg3 0 - 127478198 127479365 0,0,255
chr7 127479365 127480532 Pos5 0 + 127479365 127480532 255,0,0
chr7 127480532 127481699 Neg4 0 - 127480532 127481699 0,0,255
Best regards,
Christian
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