boxplotCCF.mutations: Plot boxplot of mutations for top genes.

In hanasusak/cDriver: Find best driver candidate genes

Description

boxplotCCF.mutations Function to plot CCF's of all mutations for top genes.

Usage

boxplotCCF.mutations(sample.mutations, result.df, topGenes = 20,
  silent = FALSE, indels = TRUE, Tumor_Sample_Barcode = NULL,
  Hugo_Symbol = NULL, CCF = NULL, Variant_Classification = NULL,
  Variant_Type = NULL, color = NULL, shape = 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. Hugo_Symbol column specifed by MAF format, which reports gene for each SNV. CCF numeric column produce by CCF function. Variant_Classification column specifed by MAF format, used to distinguish between silent and nonsilent SNVs Variant_Type columns pecifed by MAF format; is mutation SNV or InDel
result.df	a data frame with Hugo_Symbol column. Genes in this column should be ordered by importance.
topGenes	a numeric/integer value; How meny top genes from results will be ploted.
silent	a boolean value indicating should silent mutations be counted. By default it is True.
indels	a boolean value indicating should indels be counted. 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)
Hugo_Symbol	(optional) integer/numeric value indicating column in sample.mutations having gene names for reported SNVs/Indels. Default is NULL value (in this case sample.mutations should already have this column)
CCF	(optional) integer/numeric value indicating column in sample.mutations which have cancer cell fraction information for SNVs/Indels. 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)
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)
color	a numeric or character value indicating column to color the samples.
shape	a numeric or character value indicating column to use as shape for the samples.

Value

ggplot2 object

Examples

#get CCF column
sample.genes.mutect <- CCF(sample.genes.mutect)
# get background
bcgr.prob <- bcgr.combine(sample.genes.mutect, length.genes$Hugo_Symbol, length.genes$Coverd_len)
# get ranking
df1 <- bayes.risk(sample.genes.mutect, bcgr.prob, prior.sick = 0.00007) 
df2 <- bayes.driver(sample.genes.mutect, bcgr.prob,  prior.driver = 0.001) 
df.final <- combine.ranking(list(df1, df2),  min.mut = 2 )
# plot boxplot of CCF for top genes
boxplotCCF(sample.mutations=sample.genes.mutect, result.df=df.final)

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