calc.iCNA.breakpoints: calc.iCNA.breakpoints

View source: R/calc_iCNA_breakpoints.R

calc.iCNA.breakpointsR Documentation

calc.iCNA.breakpoints

Description

Author: Nicholas A Bayley Last edited by Nick: 05/28/2020 Description: A script for calculating the approximate number of breakpoints, iCNA score, and length of the genome based on segment sizes. Normalization based on length of the genome is performed by default. If no genome length is provided then the per-sample estimate of genome length is used. Input data must follow the format described here https://software.broadinstitute.org/software/igv/SEG reference: Graham, Minasyan et al. https://www.embopress.org/doi/full/10.15252/msb.20167159

NOTES: if input data follows the format described here https://software.broadinstitute.org/software/igv/SEG sep = <regex tab character> #regex tab character not explicitly indicated because it causes a waring in roxygen2 Segment_Mean is column 6 (seg_mean_index = 6) if using DepMap file CCLE_segment_cn.csv sep = "," Segment_Mean is column 5 (seg_mean_index = 5)

Usage

calc.iCNA.breakpoints(
  seg_filename,
  out_name,
  genome_size = F,
  normalize = T,
  write = T,
  not_yet_log_transformed = T,
  sep = "\t",
  seg_mean_index = 6
)

Arguments

seg_filename
out_name
genome_size
normalize
write
not_yet_log_transformed
sep
seg_mean_index

Value

out_df


graeberlab-ucla/glab.library documentation built on Oct. 28, 2024, 10:48 a.m.