workflow_oncoscan.chas: Run the standard workflow for Oncoscan ChAS files.

In yannchristinat/oncoscanR: Secondary analyses of CNV data (HRD and more)

Run the standard workflow for Oncoscan ChAS files.

Description

Run the standard workflow for Oncoscan ChAS files.

Usage

workflow_oncoscan.chas(chas.fn)

Arguments

chas.fn

Path to the text-export ChAS file

Details

Identifies the globally altered arms (\>=90% of arm altered), computes the HRD and TD+ scores. The amplification is defined as a CN subtype cntype.weakamp or cntype.strongamp. An arm is gained if of CN type cntype.gain unless the arm is amplified.

Value

A list of lists with the following elements: armlevel = list(AMP= list of arms, GAIN= list of arms, LOSS= list of arms, LOH= list of arms), scores = list(LST= number, LOH= number, TDplus= number, TD= number), file = path of the ChAS file as given by the parameter)

Examples

segs.filename <- system.file('extdata', 'chas_example.txt',
package = 'oncoscanR')
workflow_oncoscan.chas(segs.filename)

yannchristinat/oncoscanR documentation built on Oct. 26, 2024, 12:58 p.m.