computeNormalChromosomes: computeNormalChromosomes

In andrea-poletti-unibo/BOBaFIT: Refitting diploid region profiles using a clustering procedure

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)

andrea-poletti-unibo/BOBaFIT documentation built on Jan. 29, 2024, 7:23 a.m.