format_segment_data: Format segmentation data for downstream analysis using...

In TearsWillFall/variantCall: An implementation of a wrapper for variant calling using MuTECT2 and Platypus GNU/Unix based systems

Description

This function takes the segmentation data of multiple samples produced by any segment caller (mainly CNVkit) and generates a single BED file with all the segment information (chr/start/end/log2) with an additional column for sample ID. The default columns to select from original segmentation files are 1,2,3,5, which correspond to chr/start/end/log2 in CNVkit. Use argument cols_to_keep to select other columns if needed or if order is different from different segment callers.

Usage

format_segment_data(
  seg_file = "",
  dir_segment = "",
  pattern = "",
  cols_to_keep = c("chr", "start", "end", "log2", "sample"),
  output_dir = "",
  output_name = "",
  verbose = FALSE
)

Arguments

seg_file	REQUIRED Path/s to segmentation file/s. dir_segment and seg_file are mutually excluding.
dir_segment	REQUIRED Path to directory with segmentation files.
pattern	FALSE Pattern to use if directory for segmentation files is given.
cols_to_keep	[DEFAULT==c("chr","start","end","log2","sample"))] Columns to keep from original segmentation bed files [DEFAULT==c("chr","start","end","log2","sample"))]: R:DEFAULT==c(%22chr%22,%22start%22,%22end%22,%22log2%22,%22sample%22))
output_dir	Path to the output directory.
output_name	Name of the file to output.
verbose	Enables progress messages. Default False.

TearsWillFall/variantCall documentation built on Oct. 15, 2021, 8:51 p.m.