workflow_oncoscan.ascat: Run the standard workflow for ASCAT files (from oncoscan...

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

Run the standard workflow for ASCAT files (from oncoscan data).

Description

Run the standard workflow for ASCAT files (from oncoscan data).

Usage

workflow_oncoscan.ascat(ascat.fn)

Arguments

ascat.fn

Path to the text-export ASCAT file

Details

Identifies the globally altered arms (\>=90% of arm altered), computes the HRD and TD+ scores. The amplification is defined as a CN>=5. 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', 'ascat_example.txt',
package = 'oncoscanR')
workflow_oncoscan.ascat(segs.filename)

yannchristinat/oncoscanR documentation built on Oct. 27, 2023, 11:19 p.m.