find.outliers: Find hypo- and hyper-mutated samples

In liliulab/gust: Genes Under Selection In Tumors

Find hypo- and hyper-mutated samples

Description

Find hypo- and hyper-mutated samples

Usage

find.outliers(input.file.name, output.folder, output.prefix)

Arguments

input.file.name:	A VCF-formatted file to read SnpEff annotated somatic variants. This input file shall contain these fields: Tumor_Sample_Barcode, Chromosome, Start_Position, dbSNP_RS, Reference_Allele, Tumor_Seq_Allele2, FILTER, One_Consequence, Hugo_Symbol, Gene, Feature, ENSP, HGVSc, HGVSp_Short, Amino_acids, Codons, ENSP, RefSeq, Entrez_Gene_Id.
output.folder:	the folder to write the output files
output.prefix:	prefix used to name the output file as prefix.outlier.txt .

Examples

find.outliers(input.file.name='./examples/TCGA.ACC.mutect.somatic.maf.gz', output.folder='./examples/', output.prefix='TCGA.ACC');

liliulab/gust documentation built on Sept. 29, 2024, 2:52 p.m.