VT: Read summarized variation data as VariationTable object

In ShixiangWang/sigtools: Extract, Analyze and Visualize Signatures for Genomic Variations

Description

Read tab delimited MAF, CNV table and other variation files (can be plain text or gz compressed), or data.frames. Input data will be summarized in various ways.

Usage

VT(Maf = NULL, cnTable = NULL, Phenotype = NULL, refSNV = NULL,
  refINDEL = refSNV, refCNV = c("hg19", "hg38"),
  nonSyn = c("Frame_Shift_Del", "Frame_Shift_Ins", "Splice_Site",
  "Translation_Start_Site", "Nonsense_Mutation", "Nonstop_Mutation",
  "In_Frame_Del", "In_Frame_Ins", "Missense_Mutation"), segnum_min = 0,
  segnum_max = Inf, use_whole_genome = FALSE, keep_level = c("basic",
  "all", "custom"), keep_extra_cols = NULL, verbose = TRUE, ...)

Arguments

Maf	tab delimited MAF file. File can also be gz compressed. Alternatively, you can also provide already read MAF file as a data.frame.
cnTable	tab delimited file or data.frame representing CNV. It has 5 necessary columns: Chromosome (either chr# or # format, supports chr(1-22,X,Y)), Start, End, Copynumber (absolute copy number value) and Sample.
Phenotype	tab delimited file or data.frame representing phenotype data. 'Tumor_Sample_Barcode' or 'Sample' can be used as sample ID. The 'Tumor_Sample_Barcode' will be first priority if both column names exist.
refSNV	genome build version, should be 'hg19' or 'hg38'. If NULL, it will be obtained from Maf, 37 in NCBI_Build will set 'hg19' and 38 in NCBI_Build will set 'hg38'.
refINDEL	same as above.
refCNV	genome build version, should be 'hg19' or 'hg38'. Default is 'hg19'.
nonSyn	Provide manual list of variant classifications to be considered as non-synonymous. Rest will be considered as silent variants. Default uses Variant Classifications with High/Moderate variant consequences. http://asia.ensembl.org/Help/Glossary?id=535: "Frame_Shift_Del", "Frame_Shift_Ins", "Splice_Site", "Translation_Start_Site","Nonsense_Mutation", "Nonstop_Mutation", "In_Frame_Del", "In_Frame_Ins", "Missense_Mutation"
segnum_min	minimal number of copy number segments within a sample.
segnum_max	maximal number of copy number segments within a sample.
use_whole_genome	if TRUE, all genome regions for copy number data will be used. Regions with no copy number value will be set to normal copy 2. Otherwise, only regions in input data are used.
keep_level	Keep level for input data columns, you can use 'all' to keep all columns and use 'custom' to add columns except for required columns.
keep_extra_cols	extra columns to keep when keep_level set to 'custom'.
verbose	print extra messages if TRUE.

Value

a VariationTable object

Examples

library(maftools)
laml.Maf <- system.file("extdata", "tcga_laml.Maf.gz", package = "maftools")
laml <- VT(Maf = laml.Maf)

ShixiangWang/sigtools documentation built on July 17, 2019, 9:54 p.m.