annotate_simulated_variants: Annotating base substitutions generated by...

In nvolkova/MutSim: Generating cancer mutations in genes according to mutational processes

Description

@description This function generates mutations in a set of genes given the total number of mutations in samples, numbers of silent mutations per gene and total numbers of silent mutations per sample. Mutations are annotated, and numbers of silent and non-silent mutations calculated per iteration. @param variants Matrix of type character; needs to contain columns Chrom for chromosomes, Pos for substitution position, Ref for reference allele, Mut for alternative allele, and Sample for sample names. @param genome BSgenome object with relevant genome built. @param txdb A [TxDb](http://127.0.0.1:11491/help/library/GenomicFeatures/html/TxDb.html) object which serves as the annotation for distinguishing synonymous and non-synonymous variants. @param current_source seqSource argument for [predictCoding](http://127.0.0.1:11491/help/library/VariantAnnotation/help/predictCoding) annotation function. Default is "Hsapiens". @details Modifies the matrix with variants and makes it suitable for annotation using [predictCoding](http://127.0.0.1:11491/help/library/VariantAnnotation/help/predictCoding) function. Returns a matrix with additional column - Effect - which contains the prediction (unknown, synonymous, non-synonymous, or nonsense). @examples library(BSgenome.Hsapiens.UCSC.hg19) library(TxDb.Hsapiens.UCSC.hg19.knownGene) genome <- BSgenome.Hsapiens.UCSC.hg19 txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene variants <- as.matrix(data.frame(Sample = c('T1','T2'), Chrom = c('chr2','chr2'), Pos = c(1764958, 19845736), Ref = c('A', 'G'), Mut = c('T', 'A'))) annotate_simulated_variants(variants, txdb, genome)

Usage

annotate_simulated_variants(variants, txdb, genome,
  current_source = Hsapiens)

nvolkova/MutSim documentation built on May 15, 2019, 4:48 p.m.