gust: Perform GUST classification of oncogens, tumor suppressor...

In liliulab/gust: Genes Under Selection In Tumors

Perform GUST classification of oncogens, tumor suppressor genes and passenger genes from exome sequencing data.

Description

Perform GUST classification of oncogens, tumor suppressor genes and passenger genes from exome sequencing data.

Usage

gust(input.file.name, output.folder, output.prefix, steps = 1:8)

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 temporary and final prediction files.
output.prefix:	prefix used to name the temporary and final prediction files. Temporary files include prefix.outlier.txt, prefix.mut.cnt.txt, prefix.mut.filtered.txt, prefix.mut.summary.txt, prefix.error.txt, prefix.log.txt, prefix.symbol_2_cds_id.txt, prefix.genes.opt.txt, prefix.spatial.txt, prefix.fitch.txt, prefix.combined.txt, prefix.reformatted.txt, prefix.gust.txt
steps:	A vector of integers indicating which functions to execute. 1-find.outliers(), 2-parse.aggregated.mut(), 3-compute.selection.stats, 4-compute.spatial.stats(), 5-compute.fitch.stats(), 6-append.info(), 7-reformat(), 8-make.prediction(). Default to 1:8.

Examples

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

liliulab/gust documentation built on Aug. 30, 2022, 1:42 a.m.