ProteinPaint txt for bundled coding SSMs #3
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| pp_37_g <- ssm_to_proteinpaint( | ||
| maf_data = maf_37_g, | ||
| this_seq_type = "genome", | ||
| sample_type = "time_point", |
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Can you use pairing_status instead of time_point?
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Sure! However, since this is the bundled data, the pairing_status of all samples are matched.
> library(GAMBLR.data)
> meta <- get_gambl_metadata()
Using the bundled metadata in GAMBLR.data...
> table(meta$pairing_status)
matched
300
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Is this because you're only generating these files for genome data (not capture)?
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Doesn't this return quite a few rows?
meta <- get_gambl_metadata(seq_type_filter="capture")
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It does return a few rows, but all of them are matched. So, if we use sample_type = "pairing_status" we are not going to separate anything, right?
> library(GAMBLR.data)
> meta <- get_gambl_metadata(seq_type_filter = "capture")
Using the bundled metadata in GAMBLR.data...
> table(meta$pairing_status)
matched
13
Maybe you were think about the restrict data:
> meta <- GAMBLR.results::get_gambl_metadata(seq_type_filter = "capture")
> table(meta$pairing_status)
matched unmatched
527 2759
> meta <- GAMBLR.results::get_gambl_metadata(seq_type_filter = "genome")
> table(meta$pairing_status)
matched unmatched
1717 214
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Isn't the Reddy cohort in the bundled results? All of those are unmatched.
The files added by this PR were created using
ssm_to_proteinpaintfunction from this GAMBLR.utils PR.