[BioC] how to import some specific columns into R
narges [guest]
guest at bioconductor.org
Thu Apr 12 12:05:29 CEST 2012
hi
I have a huge counts file containing tags and all the related samples (129 samples) and I want to load only some columns(samples) to DGEList object not the result(counts) of all samples.
I have used scan but it does not work.
Thanks alot
Best Regards
-- output of sessionInfo():
> scan ("count.txt", what = list (0,NULL,0),skip=2,flush=TRUE)
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
scan() expected 'a real', got 'ENSG00000000005'
#############################
d <- read.table("count.txt", colClasses = c(rep("character",1),rep("integer",2), rep("null",126)),header=TRUE)
Error in methods::as(data[[i]], colClasses[i]) :
no method or default for coercing "character" to "null"
> d <- read.table("count.txt", colClasses = c(rep("character",1),rep("integer",2), rep("NA",126)),header=TRUE)
Error in methods::as(data[[i]], colClasses[i]) :
no method or default for coercing "character" to "NA"
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