exportAromaUnitPscnBinarySet: Export total and allele B signal data sets as a unified...

In aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

Export total and allele B signal data sets as a unified parent-specific copy number signal data set

Description

Export total and allele B signal data sets as a unified parent-specific copy number signal data set, where each sample is stored in one data file (contrary to the input data sets where each sample is stored in two separated files).

Usage

 ## S3 method for class 'AromaUnitTotalCnBinarySet'
exportAromaUnitPscnBinarySet(dsT, dsB="*", dataSet="*", tags="*", ...,
  rootPath="totalAndFracBData/", overwrite=!skip, skip=TRUE, verbose=FALSE)
 ## S3 method for class 'list'
exportAromaUnitPscnBinarySet(dsList, ...)

Arguments

dsT, dsB	An AromaUnitTotalCnBinarySet and an AromaUnitFracBCnBinarySet with coupled sets of samples that match up by name. If they don't match up, an exception is thrown. The allele B fraction (BAF) data set dsB is by default inferred from the total CN data set dsT.
dataSet, tags	The name and tags of the output data set. The default is to infer those from the input dsT data set.
...	Not used.
rootPath	The root path of the output data set.
overwrite, skip	Specifies whether to overwrite and/or skip already exported samples.
verbose	See Verbose.

Value

Returns an AromaUnitPscnBinarySet object.

Allele-specific CRMAv2 pipeline

A common use case is to run allele-specific CRMAv2, e.g. dsNList <- doASCRMAv2(csR), which outputs a list dsNList with elements corresponding to dsT and dsB. This output can be exported to AromaUnitPscnBinarySet by this method as dsN <- exportAromaUnitPscnBinarySet(dsNList).

Author(s)

Henrik Bengtsson

aroma.core documentation built on June 25, 2024, 1:15 a.m.