[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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