module.screen {DEComplexDisease} | R Documentation

## Screen the feature patients or genes in predicted modules

### Description

Screen feature patients or genes given by users among the predicted modules

### Usage

    module.screen(res.module, feature.patients = NULL, feature.genes = NULL,
      show.mods = NULL, show.n = 4, method = c("ratio", "fisher.test")[1],
      cores = 1)

### Arguments

`res.module` | a 'seed.module' or 'cluster.module' object returned by `seed.module` or `cluster.module`
`feature.patients` | the patients to screen
`feature.genes` | the genes to screen
`show.mods` | the modules to display
`show.n` | the number of modules to display
`method` | the method to find the most associated modules
`cores` | the thread number

### Details

This function is used to find the modules associated with the 'feature.patients' or 'feature genes'.

In current version, two methods can be used: 'ratio' and 'fisher.test'. ‘ratio' is to rank the modules based on ratio between observed overlaps and the expected overlaps that estimated using all the samples. 'fisher.test' is to use Fisher’s exact test to check the significance of association.

### Value

A plot for gene or patient overlaps with the feature genes or patients.

### Author(s)

Guofeng Meng

### Examples

    # screen the modules for feature patients.
    module.screen(seed.mod, feature.patients=sample(colnames(deg),15))

[Package DEComplexDisease version 1.2.0 Index]