parse_Battenberg: Parse Battenberg calls.

In caravagnalab/CNAqc: CNAqc - Copy Number Analysis quality check

Parse Battenberg calls.

Description

Returns two tibbles in CNAqc-ready format, one with clonal calls and the other with subclonal calls extracted by parsing the Battenberg format. This function can be used to process raw date released by PCAWG.

Usage

parse_Battenberg(x)

Arguments

x	The input dataframe, required to have the following columns: chr, from, to, battenberg_nMaj1_A, battenberg_nMin1_A, battenberg_nMaj2_A, battenberg_nMin2_A, battenberg_frac1_A, and battenberg_frac2_A.

Value

Two tibbles in CNAqc-ready format.

Examples

## Not run: 
# Load some CSV results from Battenberg
x = read.csv(....) %>% parse_Battenberg()

# Work with clonal calls (omitting mutations and other parameters here)
x = init(cna = x$clonal, ...)


# work with subclonal calls (omitting mutations and other parameters here)
x = analyze_peaks_subclonal(cna = x$subclonal, ...)

## End(Not run)

caravagnalab/CNAqc documentation built on Oct. 31, 2024, 3:54 a.m.