musicatk::create_musica() from a data frame leads to only NN as variant alleles

[ThomasGro]

Hi, I run musicatk::create_musica() from a dataframe. This results in a count table with only NN as variant alleles. I am not sure how I can get to the correct variant alleles in. It also leads to downstream errors in the signature detection step.

head(dbs.df) chr start end ref alt sample 1 1 104017 104018 CC TT ONCOLEAD_CELL_CAPAN1 2 1 149875 149876 GC CG ONCOLEAD_CELL_CAPAN1 3 1 232961 232962 TG CA ONCOLEAD_CELL_CAPAN1 4 1 362904 362905 TT GG ONCOLEAD_CELL_CAPAN1 g=select_genome("hg19") dbs_musica <- create_musica(x = dbs.df, genome = g) build_standard_table(dbs_musica, g, "DBS78", overwrite = TRUE) Building count table from DBS with DBS78 schema head(dbs_musica@count_tables$DBS78@annotation) motif mutation context AC>NN_CA AC>NN_CA AC>NN CA AC>NN_CG AC>NN_CG AC>NN CG AC>NN_CT AC>NN_CT AC>NN CT AC>NN_GA AC>NN_GA AC>NN GA AC>NN_GG AC>NN_GG AC>NN GG AC>NN_GT AC>NN_GT AC>NN GT

musica.result <- discover_signatures(musica = dbs_musica, table_name = "DBS78", num_signatures = 3, algorithm = "lda", nstart = 10, par_cores=8) Error in colSums(counts_table) : 'x' must be an array of at least two dimensions

[achevali]

Hi Thomas, It looks like your steps should work. In order to view the count table to see what might be going on, take a look at head(dbs_musica@count_tables$DBS78@count_table) If the count table data is not sensitive you can post it here to diagnose.

It's possible your chromosome chr column should have data of the form chr1 not 1. You can try modifying that and see if it solves your issue.

Please let me know if either of those are informative!

[ThomasGro]

Hi, Thank you for your swift reply.

Since I am getting the same output also when I start from the VCF file, maybe I misunderstand the format of the count table and annotation:

        motif mutation context

AC>NN_CA AC>NN_CA AC>NN CA

My interpretation is that the mutation is NN in this example and the 3´and 5´bases are C and A. That would mean that the variant allele is not defined? Or is the variant allele information in the ‘context’ field?

Thank you, Thomas Von: achevali @.> Gesendet: Friday, March 11, 2022 4:10 PM An: campbio/musicatk @.> Cc: Thomas Grombacher @.>; Author @.> Betreff: Re: [campbio/musicatk] musicatk::create_musica() from a data frame leads to only NN as variant alleles (Issue #52)

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Hi Thomas, It looks like your steps should work. In order to view the count table to see what might be going on, take a look at @.**@._table) If the count table data is not sensitive you can post it here to diagnose.

It's possible your chromosome chr column should have data of the form chr1 not 1. You can try modifying that and see if it solves your issue.

Please let me know if either of those are informative!

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[achevali]

The DBS motifs are defined here: https://cancer.sanger.ac.uk/signatures/dbs/

But I would highly recommend viewing dbs_musica@count_tables$DBS78@count_table

As this will enumerate the exact motifs and counts in a human-readable format If you have many samples you may want to try dbs_musica@count_tables$DBS78@count_table[, 1:3] to view just a few samples' counts.

[ThomasGro]

@.**@._table[, 1:3] Error in @.**@._table[, 1:3] : subscript out of bounds

@.**@.[, 1:3] motif mutation context AC>NN_CA AC>NN_CA AC>NN CA AC>NN_CG AC>NN_CG AC>NN CG AC>NN_CT AC>NN_CT AC>NN CT

And the latter leading to my confusion. But I understand now that you use the annotation as provided by Cosimc which is according to your ‘motif’ column. The ‘mutation’ column in ‘annotation’ is still confusing, and maybe should be changed to:

        motif mutation context

AC>NN_CA AC>NN_CA AC>CA NN AC>NN_CG AC>NN_CG AC>CG NN AC>NN_CT AC>NN_CT AC>CT NN

Thank you. Thomas Von: achevali @.> Gesendet: Friday, March 11, 2022 5:28 PM An: campbio/musicatk @.> Cc: Thomas Grombacher @.>; Author @.> Betreff: Re: [campbio/musicatk] musicatk::create_musica() from a data frame leads to only NN as variant alleles (Issue #52)

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The DBS motifs are defined here: https://cancer.sanger.ac.uk/signatures/dbs/

But I would highly recommend viewing @.**@._table

As this will enumerate the exact motifs and counts in a human-readable format If you have many samples you may want to try @.**@._table[, 1:3] to view just a few samples' counts.

— Reply to this email directly, view it on GitHubhttps://github.com/campbio/musicatk/issues/52#issuecomment-1065275430, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AENMOYJBS7DOG2WAYGZZGTTU7NYARANCNFSM5QPI463A. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you authored the thread.Message ID: @.***>

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