plotAllGraphs: plotAllGraphs

In laderast/surrogateMutation: Surrogate Mutations in Cancer Cells and Patients

Description

Given a surrogateTable object generated by buildSurrogateTable(), generate all surrogate graphs.

Usage

plotAllGraphs(surrogateTable, gisticCopyCalls, surrogateResults, intome)

Arguments

surrogateTable	A surrogateTable data frame generated from buildSurrogateTable()
gisticCopyCalls	When set to NULL, plotAllGraphs will look in the surrogateResults$mutCopyFrames object for the copy number calls for each gene.
surrogateResults
intome

Value

An SVG file generated for each line in the surrogateTable data frame. The SVG files will have the format (Sample)-GeneName.svg.

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.
##load surrogate result object
library(DLBCL)
data(interactome)

data(surrogateResult)
surrogateTable <- buildSurrogateTable(surrogateResult)

##filter the surrogate table based on p-value and return surrogate mutations greater than 5.
filteredSurrTable <- surrogateTable[surrogateTable$pvalue < 0.05 & surrogateTable$neighbor > 3,]
filteredSurrTable

#plot all graphs in current working directory
#be careful with the size of the table you pass to plotAllGraphs - it may generate
#a huge number of files.
plotAllGraphs(filteredSurrTable, surrogateResult, intome=interactome)

laderast/surrogateMutation documentation built on May 20, 2019, 7:33 p.m.