DRrefit: DRrefit

In bioinformatic-seragnoli/BOBaFIT: Refitting diploid region profiles using a clustering procedure

DRrefit

Description

This function refits the diploid region of input copy number profiles (segments - BED file)

Usage

DRrefit(
  segments_chort,
  chrlist,
  maxCN = 6,
  clust_method = "ward.D2",
  verbose = FALSE
)

Arguments

segments_chort	data.frame formatted with correct column names
chrlist	list of normal chromosome arms (pathology-specific)
maxCN	threshold of max copy number to consider. By default is 6
clust_method	clustering method. By default is "ward.D2"
verbose	print information about the processes of the function. By default is FALSE

Value

Return two data frames, one is the DRrefit-corrected segments and the other is the samples report. See the vignette for data frame descriptions.

Examples

data("TCGA_BRCA_CN_segments")

chr_list <- c("10q","11p","12p","19q","1p","21q","2q","3p","4p","4q","6p","6q","7p" )

results <- DRrefit(segments_chort = TCGA_BRCA_CN_segments, 
                   chrlist = chr_list)

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