+
+
+
+
+
+
+
+
+
The pbta-histologies.tsv file contains a tumor_ploidy column, which is tumor ploidy as inferred by ControlFreeC. The copy number information should be interpreted in the light of this information (see: current version of Data Formats section of README).
+
This notebook adds ploidy information to the CNVkit results and adds a status column that defines gain and loss broadly.
+
+
+
+
library(dplyr)
+
+
+
+Attaching package: 'dplyr'
+
+
+
The following objects are masked from 'package:stats':
+
+ filter, lag
+
+
+
The following objects are masked from 'package:base':
+
+ intersect, setdiff, setequal, union
+
+
+
+
+
Read in data
+
+
+
+
cnvkit_file <- file.path("..", "..", "data", "pbta-cnv-cnvkit.seg.gz")
+cnvkit_df <- readr::read_tsv(cnvkit_file)
+
+
+
Parsed with column specification:
+cols(
+ ID = col_character(),
+ chrom = col_character(),
+ loc.start = col_double(),
+ loc.end = col_double(),
+ num.mark = col_double(),
+ seg.mean = col_double(),
+ copy.num = col_double()
+)
+
+
+
+
+
+
+
histologies_file <- file.path("..", "..", "data", "pbta-histologies.tsv")
+histologies_df <- readr::read_tsv(histologies_file)
+
+
+
Parsed with column specification:
+cols(
+ .default = col_character(),
+ OS_days = col_double(),
+ age_last_update_days = col_double(),
+ normal_fraction = col_double(),
+ tumor_fraction = col_double(),
+ tumor_ploidy = col_double()
+)
+
+
+
See spec(...) for full column specifications.
+
+
+
+
+
+
+
Add status column
+
This is intended to mirror the information contained in the ControlFreeC output.
+
+
+
+
add_ploidy_df <- add_ploidy_df %>%
+ mutate(status = case_when(
+ # when the copy number is less than inferred ploidy, mark this as a loss
+ copy.num < tumor_ploidy ~ "loss",
+ # if copy number is higher than ploidy, mark as a gain
+ copy.num > tumor_ploidy ~ "gain",
+ copy.num == tumor_ploidy ~ "neutral"
+ ))
+
+head(add_ploidy_df, 10)
+
+
+
+
+
+
+
+
+
Write to scratch
+
+
+
+
output_file <- file.path("..", "..", "scratch", "cnvkit_with_status.tsv")
+readr::write_tsv(add_ploidy_df, output_file)
+
+
+
+
+
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+
+
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+