is_valid_clinicalfeaturefile: Is a clinical_feature_file valid for a given maf

In CCICB/CRUX: Easily explore patterns of somatic variation in cancer using 'CRUX'

Is a clinical_feature_file valid for a given maf

Description

Runs read.maf with a given clinicalData and maf object pair and returns TRUE ONLY if the clinicalData file is appropriate for the given MAF. If maf object is not valid, this function will also return FALSE. By using clinicalData=NULL the function allows testing validity of a MAF file in Isolation.

Usage

is_valid_clinicalfeaturefile(clinicalData, maf)

Arguments

clinicalData	Clinical data associated with each sample/Tumor_Sample_Barcode in MAF. Could be a text file or a data.frame. Default NULL.
maf	tab delimited MAF file. File can also be gz compressed. Required. Alternatively, you can also provide already read MAF file as a dataframe.

Details

If clinical feature file has duplicated Tumor_Sample_Barcodes, only the first entry is considered and the file is still 'valid'.

Value

True / False (boolean)

CCICB/CRUX documentation built on Jan. 28, 2024, 10:12 p.m.