runCaSpER: runCaSpER()

In akdess/CaSpER: Identify large-scale CNV events from single cell or bulk RNA-Seq data

Description

Main casper function that performs a pairwise comparison of all scales from BAF and expression signals to ensure a coherent set of CNV calls.

Usage

runCaSpER(object, removeCentromere = T, cytoband = object@cytoband,
  method = "iterative")

Arguments

object	casper object
removeCentromere	boolean values determining if centromere regions should be removed from the analysis
cytoband	cytoband information downloaded from UCSC hg19: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cytoBand.txt.gz hg38:http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBand.txt.gz
method	iterative or fixed method. Fixed performs CNV calls on desired baf and expression scale whereas iterative performs pairwise comparison of all expression and baf scale pairs. Iterative method is recommendend. (default: iterative)

Value

list of objects

akdess/CaSpER documentation built on April 8, 2021, 8:59 a.m.