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UMCUGenetics / mutSigExtractor

An R package for extracting mutational signatures from vcf files
GNU General Public License v3.0
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.Call2 error #9

Open yoonjuy opened 1 year ago

yoonjuy commented 1 year ago

Using a DRAGEN Enrichment-created VCF as the input, I obtain the following error:

Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord, : solving row 1224: 'allow.nonnarrowing' is FALSE and the supplied start (181121150) is > refwidth + 1

Thanks for your help in advance.

luannnguyen commented 1 year ago

Hi,

What ref genome are you using? The default is hg19, but if youre using hg38 you'll have to manually specify the hg38 BSGenome.

Luan

yoonjuy commented 1 year ago

Gotcha--that did the trick. Thank you!

Sorry one more (separate) question--is there a plot function in this package?

Thanks again.

luannnguyen commented 1 year ago

No problem!

Yes you can use plotContexts(x), where x is a matrix/dataframe with rows being samples and cols being mutation contexts. See: https://github.com/UMCUGenetics/mutSigExtractor/blob/1dfd05d1f187074ddfcbac2418212cc5ba264e86/R/plotContexts.R#L68