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Update focal-cn-preparation to use consensus SEG file in data download #1130

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Update focal-cn-preparation to use consensus SEG file in data download #1130

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jaclyn-taroni Jan 11, 2021
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jaclyn-taroni Jul 19, 2021
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jaclyn-taroni Aug 9, 2021
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Try using the consensus seg in the download file
jaclyn-taroni Aug 9, 2021
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jaclyn-taroni Aug 9, 2021
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4 changes: 1 addition & 3 deletions analyses/focal-cn-file-preparation/02-add-ploidy-consensus.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -41,9 +41,7 @@ if(!dir.exists(output_dir)) {
```

```{r}
# TODO: the consensus SEG file is not currently in the data download -- when it
# gets included we will have to change the file path here
consensus_seg_file <- file.path("..", "copy_number_consensus_call", "results",
consensus_seg_file <- file.path("..", "..", "data",
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@jharenza and @kgaonkar6 - is there any reason (that you are aware of) that prohibits me from making this change at this point?

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I do not think so - the latest file is in the download.

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@jaclyn-taroni jaclyn-taroni Aug 10, 2021 •
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We probably need to wait until all the v20 CNV changes go through though? Or would just getting #1123 through -> updating the release (if not done yet) be sufficient?

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I've updated v20 release data with the latest consensus seg with #1123 b9284650be04df3538e6c6dba29b8eb0 pbta-cnv-consensus.seg.gz

I added the relative path so that we can run the code while running all the preprocessing steps of subtyping, so maybe we can add a logic to change to relative path or not within the if (params$base_run ==0)

OpenPBTA-analysis/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.Rmd

Lines 48 to 58 in a6281c2

```{r}
# TODO: the consensus SEG file is not currently in the data download -- when it
# gets included we will have to change the file path here
consensus_seg_file <- file.path("..", "copy_number_consensus_call", "results",
"pbta-cnv-consensus.seg.gz")
if ( params$base_run ==0 ){
histologies_file <- file.path("..", "..", "data", "pbta-histologies.tsv")
} else {
histologies_file <- file.path("..", "..", "data", "pbta-histologies-base.tsv")
}

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In which scenario would you use the file in analyses/copy_number_consensus_call/results? When you use pbta-histologies-base.tsv?

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yes, we will rerun the consensus seg file module first so the latest consensus seg file can be used as input for the focal-cn module

"pbta-cnv-consensus.seg.gz")
histologies_file <- file.path("..", "..", "data", "pbta-histologies.tsv")

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