detectTERM: Detecting TE-regulation modules from the constructed...

In bioinfoxh/term: Identification of Translational Efficiency Regulated Modules with ribosome profiling data

Description

Detecting TE-regulation modules from the constructed multi-layer differential expression network

Usage

detectTERM(ppi, DEstat, TEstat, num_seed = 100, minModSize = 10,
  permTimes = 100, modularity_p = 0.05, maxModOvlp = 0.5)

Arguments

ppi	a matrix/dataframe containing gene-gene interactions in two columns
DEstat	a list including two dataframes of statistics and p-values of differential expression for mRNAs and RPFs respectively
TEstat	a vector of differential translation significance of genes
num_seed	the number of seed genes used for searching modules from multi-layer networks, with default value 100
minModSize	the number of minimum genes within a module, with default value 10
permTimes	permutation times for calculating modulatrity significance of modules, with default value 100
modularity_p	threshold for modulatrity significance, with default value 0.05
maxModOvlp	threshold for meetmin index defining the overlapping between modules, with default value 0.5

Value

a list of results including a dataframe of the multi-layer network with edge weights in each network as well as the average weight and a list of identified TE-regulated modules

Examples

detectTERM()
detectTERM(ppi, DEstat, TEstat,num_seed=100,minModSize=10,permTimes=100,modularity_p=0.05,maxModOvlp=0.5)

bioinfoxh/term documentation built on May 23, 2019, 6:06 p.m.