calculateDTE: Calculate the differential expression of mRNAs and RPFs, and...

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

Description

Calculate the differential expression of mRNAs and RPFs, and the differential translation of genes.

Usage

calculateDTE(raw_rna, raw_ribo, rna_label, ribo_label, baseLevel,
  minCounts = 10, minCountsProportion = 1)

Arguments

raw_rna	raw RNA-seq read counts
raw_ribo	raw Ribo-seq read counts
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
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

Value

a dataframe consists of DESeq2 results of mRNA and RPF differential expression and Riborex results of differential translation

Examples

calculateDTE()
calculateDTE(raw_rna, raw_ribo, rna_label, ribo_label, baseLevel, minCounts=10, minCountsProportion=1 )

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