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Mimoeschen 04-17-2013 12:21 PM

RepeatMasker track UCSC in R

I have problems loading the repeatmasker track from UCSC into R. I try to use the makeFeatureDbFromUCSC function from the GenomicFeatures package. The R code and the corresponding error message is below.
Am I doing something wrong, or is there a problem with the track?

Thank you very much!



repdb <- makeFeatureDbFromUCSC(genome= "hg19", track="rmsk", table="rmsk", chromCol="genoName", chromStartCol="genoStart", chromEndCol="genoEnd")


Download the rmsk table ...

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
line 3606345 did not have 17 elements

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