PATHChange (version 1.0)

PATHChange: Determination of differentially expressed pathways using multi-statistic comparison

Description

This is the main function of the PATHChange package. It applies to each histological comparison selected that the three non-parametric tests (Bootstrap, Fisher's exact and Wilcoxon signed-rank).

Usage

PATHChange(path, MeanData, writeCSV, writeRDS, destDIR)

Arguments

path

List of pathways previously generated by the function PATHChangeList.

MeanData

List of the results of the histological comparisons chosen by the user (It can be calculated by the function PATHChangeDat).

writeCSV

TRUE for write a .csv file result

writeRDS

TRUE for write a .rds file result

destDIR

Destination folder for .csv and .rds files.

Value

p.value

Results

Details

The approach is a multiple comparison experiment since it involves several pathways, then PATHChange corrects the false discovery rate (FDR) based on Benjamini-Hochberg algorithm.

See Also

PATHChangeList, PATHChangeDat

Examples

require(rlist)
path<-list.load(system.file("extdata", "path.rds", package = "PATHChange"))[c(1:10)]
MeanData<-list.load(system.file("extdata", "MeanData.rds", package = "PATHChange"))
  
## Not run: PATHChange(path=path, MeanData=MeanData, writeCSV=FALSE, writeRDS=FALSE)
## Not run: p.value <- list.load(file.path(tempdir(),"pValue.rds"))