PATHChange: Determination of differentially expressed pathways using...

In PATHChange: A Tool for Identification 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.

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.

Value

p.value

Results

Author(s)

Carla A. R. S. Fontoura

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"))

PATHChange documentation built on May 1, 2019, 10:20 p.m.