module.screen: Screen the feature patients or genes in predicted modules

View source: R/module.screen.R

module.screenR 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))

menggf/DEComplexDisease documentation built on June 30, 2022, 1:47 p.m.