snvinGene: snvinGene

Description Usage Arguments Details

View source: R/snvinGene.R

Description

Plot all snvs found in a given gene. A 'gene_lengths' file must be provided with the following fields (cols 1..6 required) gene length chrom start end tss scaling_factor This can be generated using the script 'script/genomic_features.pl' and a genome .gtf file

Usage

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snvinGene(..., snv_data = NULL, gene_lengths = "data/gene_lengths.txt",
  gene2plot = "kuz", annotated = TRUE, col_by_status = TRUE,
  write = FALSE)

Arguments

gene_lengths

File containing all genes and their lengths (as generated by 'script/genomefeatures.pl') [Default 'data/gene_lengths.txt']

gene2plot

Name of the gene to plot

Details

Plot all snvs found in a given gene


nriddiford/mutationProfiles documentation built on Nov. 7, 2021, 12:14 a.m.