inferDriverDominanceScore: Infer the Driver Dominances Scores for Patients and Genes.
In qingjian1991/THindex: Tumor Heterogeneity Index Estimating

inferDriverDominanceScore

R Documentation

Infer the Driver Dominances Scores for Patients and Genes.

Description

Infer the Driver Dominances Scores for Patients and Genes.

Usage

inferDriverDominanceScore(
  maf,
  tsb = NULL,
  driver = NULL,
  topGenes = 10,
  vafCol = NULL,
  segFile = NULL,
  ignChr = NULL,
  minVaf = 0,
  maxVaf = 1,
  useSyn = FALSE
)

Arguments

`maf`	an `MAF` object generated by `read.maf`
`tsb`	specify sample names (Tumor_Sample_Barcodes) for which clustering has to be done.
`driver`	The driver genes list(Hugo_Symbol), defaults setting the topGenes
`topGenes`	if `driver` is NULL, uses top n number of most frequently mutated genes. Defaults to 10.
`vafCol`	manually specify column name for vafs. Default looks for column 't_vaf'
`segFile`	path to CBS segmented copy number file. Column names should be Sample, Chromosome, Start, End, Num_Probes and Segment_Mean (log2 scale).
`ignChr`	ignore these chromosomes from analysis. e.g, sex chromsomes chrX, chrY. Default NULL.
`minVaf`	filter low frequency variants. Low vaf variants maybe due to sequencing error. Default 0. (on the scale of 0 to 1)
`maxVaf`	filter high frequency variants. High vaf variants maybe due to copy number alterations or impure tumor. Default 1. (on the scale of 0 to 1)
`useSyn`	Use synonymous variants. Default FALSE.