maf.summary: maf.summary

In margarethannum/gnomeR: What the Package Does (One Line, Title Case)

Description

Creates a set of plot summarising a maf file.

Usage

maf.summary(maf, mut.type = "SOMATIC")

Arguments

maf	the names of the segment files to be loaded and processed (Note must end in ".Rdata").
mut.type	The mutation type to be used. Options are "SOMATIC", "GERMLINE" or "ALL". Note "ALL" will keep all mutations regardless of status (not recommended). Default is SOMATIC.

Value

p.class Barplot of counts of each variant classification

p.type Barplot of counts of each variant type

p.SNV Histogram of counts of each SNV class

p.patient.variant Histogram of counts variants per patient

p.variant.bp Boxplot of the distribution of variant classification per patient

p.variant.dist Boxplot of the relative proportion of each variant class in individual patients

p.variant.dist.bar Stacked barplot of the variants distribution in all patients

p.SNV.dist Boxplot of the relative proportion of each SNV class in individual patients

p.corr Correlation heatmap of the top 10 genes

p.comut Heatmap of the comutation of the top 10 genes

Examples

library(gnomeR)
all.plots <- maf.summary(maf=mut)

margarethannum/gnomeR documentation built on Feb. 26, 2020, 8:16 p.m.