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

In DEComplexDisease: A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis

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))

DEComplexDisease documentation built on Nov. 8, 2020, 6:42 p.m.