<remote-error in ppm[snp.seq, ]: subscript out of bounds>

[ooiwf]

Hi, I ran motifbreakR with the following codes: snv = snps.from.file(file = 'snv.bed', search.genome= BSgenome.Hsapiens.UCSC.hg19, format = 'bed') result = motifbreakR( snpList = snv, filterp = T, pwmList = hocomoco, threshold = 1e-4, method = 'ic', bkg = c(A=0.25, C=0.25, G = 0.25, T= 0.25), BPPARAM = BiocParallel::bpparam()) when I enter the variable name 'result' in the R console, I found this: <remote-error in ppm[snp.seq, ]: subscript out of bounds>

The .bed file contains the following data: chr20 29653903 29653904 chr20:29653904:A:C 0 +

[Simon-Coetzee]

Okay so I think I figured out what was going wrong with that SNP, it's right on the edge of a region in the reference genome full of NNNNN, which I couldn't look up in the PWMs (as they don't contain N), but I think I resolved this by having the PWMs include N as a letter with a score of 0. I will push to Bioconductor when I've had more chance to test, but the version here has been updated.

Let me know if it works for you, and I'll close this issue.

[ooiwf]

Hi Simon, I reinstalled the library from github and rerun using the same data. The execution seems to be in debug mode, where Browse[2]> appears while running result = motifbreakR( snpList = snv, filterp = T, pwmList = hocomoco, threshold = 1e-4, method = 'ic', bkg = c(A=0.25, C=0.25, G = 0.25, T= 0.25), BPPARAM = BiocParallel::bpparam()) To complete the execution, i need to press 'ENTER' multiple times.

In addition to this, I also encounter other error when more data are used. Error in validObject(.Object) : invalid class âMotifListâobject: all matrices must have 4 rows

[Simon-Coetzee]

Okay, I think i resolved that, the motifList object wasn't validating at the end b/c it now had 5 rows (including the Ns), so I have that clean up before exit. - also removed the browser()'s