computeNormalChromosomes: computeNormalChromosomes

View source: R/computeNormalChromosomes.R

computeNormalChromosomesR Documentation

computeNormalChromosomes

Description

This function compute the DRrefits' input "chromosome list". It is a vector that contains the chromosomal arms considered "normal" in the cohort of samples tested (BED file), under a specific tolerance value

Usage

computeNormalChromosomes(
  segments,
  tolerance_val = 0.15,
  maxCN = 6,
  min_threshold = 1.6,
  max_threshold = 2.4,
  verbose = FALSE
)

Arguments

segments

data.frame formatted with correct column names

tolerance_val

decimal value of alteration frequency. By default is 0.15

maxCN

threshold of max copy number to consider. By default is 6

min_threshold

minimum threshold to define a normal CN. By default is 1.60

max_threshold

maximum threshold to define a normal CN. By default is 2.40

verbose

print information about the processes of the function. By default is FALSE

Value

vector with chromosome names and plot with the alteration rate of each chromosomal arms

Examples

data("TCGA_BRCA_CN_segments")
chr_list <- computeNormalChromosomes(segments = TCGA_BRCA_CN_segments)

bioinformatic-seragnoli/BOBaFIT documentation built on Jan. 29, 2024, 10:27 a.m.