exportAromaUnitPscnBinarySet: 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

"exportAromaUnitPscnBinarySet"(dsT, dsB="*", dataSet="*", tags="*", ..., rootPath="totalAndFracBData/", overwrite=!skip, skip=TRUE, verbose=FALSE) "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).