mutcellsummary: mutcellsummary

In SMDIC: Identification of Somatic Mutation-Driven Immune Cells

mutcellsummary

Description

Function 'mutcellsummary' is a generic function used to produce summaries of the results of 'mutcorcell' function.

Usage

mutcellsummary(mutcell, mutmatrix, cellmatrix)

Arguments

mutcell	The result of 'mutcorcell' funtion.
mutmatrix	A binary mutations matrix, which can not only come from the maf2matrix function, but also any binary mutations matrix, in which 1 represents any mutation occurs in a particular gene in a particular sample, otherwise the element is 0.
cellmatrix	Cell abundance matrix

Value

The result summaries have four columns. The first column is somatic mutant gene names, the second column is the immune cell names driven by the somatic mutation, the third column is the number of the immune cell, the fourth column is the mutation rate.

Examples

# get result of `mutcorcell` funtion
mutcell<-GetExampleData("mutcell")

#get cell abundance matrix which is the result of exp2cell function
cellmatrix<-GetExampleData("cellmatrix")

# get the binary mutations matrix
mutmatrix<-GetExampleData("mutmatrix") # A binary mutations matrix

#perform the function mutcellsummary
summary<-mutcellsummary(mutcell = mutcell,mutmatrix = mutmatrix,cellmatrix=cellmatrix)

SMDIC documentation built on Aug. 29, 2023, 5:11 p.m.