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Old 04-17-2013, 12:21 PM   #1
Mimoeschen
Junior Member
 
Location: London

Join Date: Feb 2013
Posts: 3
Default RepeatMasker track UCSC in R

Hi,

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!

input:

library(GenomicFeatures)

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



output:

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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bioconductor, genomicfeatures, makefeaturedbfromucsc, repeatmasker, ucsc

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