weightAveChr: Calculate the chromosome instability from the segment-level...

In ibphuangchen/genomicWidgets: Useful SCNA and DNA methylation analysis tools

Description

Calculate the chromosome instability from the segment-level SCNA data

Usage

weightAveChr(
  segDf,
  genomeVersion = "hg38",
  option = "abs",
  chrDf = NULL,
  nThread = NULL,
  ...
)

Arguments

segDf	segment-level SCNA data frame. This is usually the same input as GISTIC2. Make sure that there are these columns: "sample", "chromosome", "start", "end", "log2".
genomeVersion	the genome version by which SCNA data were generated, should be either 'hg19' or 'hg38'. Default is 'hg38'.
option	choose how to calculate chromosome instability, should be one of 'abs', 'amp', 'del' or 'origin'. If 'abs' (default), both CN deletions and amplifications will contribute to the instability score. If 'amp', only CN amplifications will be considered. If 'del', only CN deletions will be considered. If 'origin', CN deletions and amplifications will be canceled out for each other, compared to 'abs' where the absolute CN deletions and CN amplifications will be added up.
chrDf	a data frame specifying what genomic ranges should be considered for the instability score calculation. Three columns should be specified: "chromosome", "start" and "end. If NULL (default), the whole chromosome will be used to calculated the instability score.
...	additional parameter to for makeCluster. If you used a Linux or MacOS, it is proper to add type='FORK'.

Value

a data frame with columns representing each samples in segDf, and rows representing instability scores specified by the input chrDf

Examples

hnsccSegfile <- system.file("extdata", "CPTAC3_HNSCC_SCNA_segment_level.tsv", package = "genomicWidgets")
hnsccSegDf <- read.table(hnsccSegfile, header = TRUE)
weightAveChr(hnsccSegDf, genomeVersion = 'hg38') 
 

ibphuangchen/genomicWidgets documentation built on Aug. 20, 2021, 10:55 a.m.