term: The main function performs the whole pipeline of TERM to...

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

Description

The main function performs the whole pipeline of TERM to identify TE-regulated modules.

Usage

term(raw_rna, raw_ribo, rna_label, ribo_label, baseLevel, raw_ppi,
  minCounts = 10, minCountsProportion = 1, num_seed = 100,
  minModSize = 10, permTimes = 100, modularity_p = 0.05,
  maxModOvlp = 0.5)

Arguments

raw_rna	raw RNA-seq read counts matrix
raw_ribo	raw Ribo-seq read counts matrix
rna_label	the experiment conditions corresponding to the samples in raw_rna
ribo_label	the experiment conditions corresponding to the samples in raw_ribo
baseLevel	the condition used as the base level for comparisons of differential expression and differential translation
raw_ppi	a matrix/dataframe containing gene-gene interactions in two columns
minCounts	the number of minimum read count of a gene in a sample, with default value 10
minCountsProportion	the proportion of samples where a gene exhibits read counts larger than the minCounts in a same condition, with default value 1
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 mRNA and RPF differential expression and differential translation of genes, a dataframe of the multi-layer network with edge weights in each network as well as the average weight, a list of identified TE-regulated modules

Examples

term()
term(raw_rna, raw_ribo, rna_label, ribo_label, baseLevel, raw_ppi, minCounts=10, minCountsProportion=1,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.