plotMutChange: Plot mutations pattern frequncies.

In hanasusak/cDriver: Find best driver candidate genes

Description

plotMutChange Function to plot frequency of mutation changes.

Usage

plotMutChange(sample.mutations, silent = TRUE, fill = TRUE,
  Tumor_Sample_Barcode = NULL, Variant_Type = NULL,
  Variant_Classification = NULL, Reference_Allele = NULL,
  Tumor_Seq_Allele2 = NULL)

Arguments

sample.mutations	data frame in MAF like format. Columns (with exactly same names) which sample.mutations should have are: Tumor_Sample_Barcode column specifed by MAF format, reporting for each SNV in wich patient was found. Variant_Type columns pecifed by MAF format; is mutation SNV or InDel Variant_Classification column specifed by MAF format, used to distinguish between silent and nonsilent SNVs Reference_Allele column specifed by MAF format, represents referent allele Tumor_Seq_Allele2 column specifed by MAF format, represents alternative allele
silent	a boolean value indicating should silent mutations be counted. By default it is True.
fill	a boolean value indicating should plot only represent proportion between 3 types of mutations, not counts. By default it is True
Tumor_Sample_Barcode	(optional) integer/numeric value indicating column in sample.mutations which have sample ids for SNVs/Indels. Default is NULL value (in this case sample.mutations should already have this column)
Variant_Type	(optional) integer/numeric value indicating column in sample.mutations which contains indormation if mutations is SNV or InDel . Default is NULL value (in this case sample.mutations should already have this column)
Variant_Classification	(optional) integer/numeric value indicating column in sample.mutations which contain classification for SNV (Silent or not). Default is NULL value (in this case sample.mutations should already have this column)
Reference_Allele	(optional) integer/numeric value indicating column in sample.mutations which contain reference alleles. Default is NULL value (in this case sample.mutations should already have this column)
Tumor_Seq_Allele2	(optional) integer/numeric value indicating column in sample.mutations which contain alternative alleles. Default is NULL value (in this case sample.mutations should already have this column)

Value

ggplot2 object

Examples

# plot SNVs changes patterns
plotMutChange(sample.genes.mutect)
# plot SNVs changes patterns only for non silent mutaions
plotMutChange(sample.genes.mutect, silent=FALSE, fill=FALSE)

hanasusak/cDriver documentation built on May 17, 2019, 2:27 p.m.