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Update manta FILTER=='PASS' Part3 : oncoprint rerun #1116

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Jul 22, 2021
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9 changes: 8 additions & 1 deletion analyses/oncoprint-landscape/01-map-to-sample_id.R
Original file line number Diff line number Diff line change
Expand Up @@ -328,7 +328,14 @@ cnv_df <- cnv_df %>%
mutate(Tumor_Sample_Barcode = sample_id) %>%
rename(Variant_Classification = status,
Hugo_Symbol = gene_symbol) %>%
select(Hugo_Symbol, Tumor_Sample_Barcode, Variant_Classification)
select(Hugo_Symbol, Tumor_Sample_Barcode, Variant_Classification) %>%
# mutate loss and amplification to Del and Amp to fit Maftools format
dplyr::mutate(Variant_Classification = dplyr::case_when(Variant_Classification == "deep deletion" ~ "Del",
Variant_Classification == "amplification" ~ "Amp",
TRUE ~ as.character(Variant_Classification))) %>%
# only keep Del and Amp calls
filter(Variant_Classification %in% c("Del", "Amp"))


# Write to file
readr::write_tsv(cnv_df, cnv_output)
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