.Call2 error

[yoonjuy]

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]

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]

Gotcha--that did the trick. Thank you!

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

Thanks again.

[luannnguyen]

No problem!

Yes you can use plotContexts(x), where x is a matrix/dataframe with rows being samples and cols being mutation contexts.
See:

mutSigExtractor/R/plotContexts.R

Line 68 in 1dfd05d

plotContexts <- function(