deseq2: deseq2

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

deseq2

Description

deseq2

Usage

deseq2(Row_count_matrix, method = "BH")

Arguments

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

References

Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biology 15(12):550 (2014)

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)
deseq2("Row_count_data.txt")

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