rcquan / bedgraph2dmr Goto Github PK

I just tried to use these scripts and ran into a problem with bsseq not taking in the new bedgraph format as it lacks count columns.

From http://bioconductor.org/packages/release/bioc/manuals/bsseq/man/bsseq.pdf:

Please note that the ".bedGraph" file created in recent versions of Bismark
(v>=0.10.0) is notsuitable for analysis with bsseq because it only contains the "methylation percentage"
and not "count methylated" nor "count unmethylated".

The relevant information is in the coverage (.cov) files that bismark now puts out. Renaming these files to .bedGraph did allow read.bismark to progress.

I ended up getting another error later, though I didn't really try to resolve this and it may be unrelated:

Error in which(rowSums(methCov[, BSmooth_obj$type %in% c("control", "normal")] >= :
error in evaluating the argument 'x' in selecting a method for function 'which': Error in rowSums(methCov[, BSmooth_obj$type %in% c("control", "normal")] >= :
'x' must be an array of at least two dimensions

Hi Ryan,

When I run the program I'm getting the following error message after entering the control and case inputs: Error in density.default(tstat) : 'x' contains missing values. However if I enter "case" for the control input and "control" for the case input I don't get this error message and results are outputted. I have more control samples than case samples and I'm using the "group2" option for est_var.

Any help is greatly appreciated! Thanks!

Jen