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zhqingit / giremi

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
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error in R out files #42

Open mj163163 opened 6 years ago

mj163163 commented 6 years ago

Dear, after running the programme, I got this:

dat <- read.table(file=finput,header=F,row.names=1,comment.char="")

dat <- read.table(file=finput,header=T,comment.char="") Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 1 did not have 24 elements Calls: read.table -> scan Execution halted

Could you give me some demo data to run this programme? like snp file, bam files. How can I get snp files for -l ? I know little about snp, thank you!

Best, Doc. Fan

userbz commented 6 years ago

I encountered the same problem and made a temporary solution.

The problem is that the R-script cannot handle missing values created by the GIREMI replace the line for data loading by dat <- read.csv(file=finput,header=T,comment.char="", sep='\t', na.strings=c("","NA")) will do the trick. However, I ended up with other problem with empty training set, due to large p-values. Anyway. the pro-processing script is confusing in my opinion.