pathVarTwoSamplesCont {pathVar} | R Documentation

## Compares the distribution of genes in each pathway for two groups of samples that you define.

### Description

Compares the distribution of genes in each pathway for two groups of samples that you define.

### Usage

    pathVarTwoSamplesCont(dat.mat, pways,groups,boot=1000,varStat=c("sd","mean", "mad", "cv"))

### Arguments

`dat.mat` | `matrix` with the genes on the rows and the samples on the columns.
`pways` | `list` which contains a `vector` of pathway IDs, a `vector` of pathway names, and a `list` of genes in each pathway.
`groups` | `vector` indicating the amount of samples and replicates of each sample.
`boot` | number of bootstraps to be performed.
`varStat` | a string specifying the type of variability summary statistic to perform. The options are "sd", "mean", "mad", or "cv".

### Details

This function splits the samples into two groups that you define. It compares the density of the variability (SD, MAD, CV) or of the mean of the genes in a pathway from group 1 with the density from group 2. For that, it uses the bootstrap Kolmogorov-smirnov test. You can give your own list of pathways (using the output of `makeDBList`) or use Reactome and KEGG pathways that are already included.

### Value

A `geneDistributionSet2` object is returned.

### Author(s)

Laurence de Torrente, Samuel Zimmerman, Jessica Mar

### Examples

    # we run the 2 samples analysis on the first 10 pathways from kegg
    pways.kegg.10pways <- lapply(pways.kegg, function(x) x[1:10])
    results_2samples=pathVarTwoSamplesCont(bock,pways.kegg.10pways,groups=as.factor(c(rep(1,10),rep(2,10))),boot=1000,varStat="sd")

[Package pathVar version 1.20.0 Index]