SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   RepeatMasker track UCSC in R (http://seqanswers.com/forums/showthread.php?t=29408)

Mimoeschen 04-17-2013 12:21 PM

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


All times are GMT -8. The time now is 10:09 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.