edger: edgeR

In Kan-E/rnaseqviewer: Toolkit for automated, systematic, and integrated RNA-seq DEG analysis

edgeR

Description

edgeR

Usage

edger(Row_count_matrix, method = "BH")

Arguments

Row_count_matrix	Row Count matrix txt file (Not normalized count matrix)
method	BH, Qvalue, or IHW

References

Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140

Nikolaos Ignatiadis, Bernd Klaus, Judith Zaugg and Wolfgang Huber (2016): Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nature Methods 13:577, doi: 10.1038/nmeth.3885

John D. Storey, Andrew J. Bass, Alan Dabney and David Robinson (2021). qvalue: Q-value estimation for false discovery rate control. R package version 2.26.0. http://github.com/jdstorey/qvalue

Examples

library(rnaseqviewer)

data(Row_count_data)
write.table(Row_count_data, file = "Row_count_data.txt", sep = "\t", quote = FALSE)
edger("Row_count_data.txt")

Kan-E/rnaseqviewer documentation built on May 30, 2022, 10:34 a.m.