DEAnalysis: Routine analysis of transcriptome sequencing

In zexllin/lncRNAtools: Do lncRNA bioinformatics Advanced analysis,includes routine analysis of mRNA/miRNA

Description

Difference analysis of transcriptome sequencing

Usage

DEAnalysis(countDataRaw, Group, control, filter = TRUE, lognormdata = TRUE)

Arguments

countDataRaw	Expression matrix of transcriptome sequencing
Group	a vector of sample group
control	Set up control group
filter	a logical ,filter gene use cpm
lognormdata	a logical,rlogTransformation for normdata

Value

a list,data frame of Difference analysis,normlized Expression matrix , and normlized Expression matrix after log Transformation

Author(s)

zexl

References

Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010 Jan 1;26(1):139-40.
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic acids research. 2015 Jan 20; 43(7):e47-e47.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology. 2014 Dec 5; 15(12):550. @author zexl @examples DeResult<-DEAnalysis(Counts, group,control='Z') DEGAll<-DeResult[[1]] normData<-DeResult[[2]] normData_log <- assay( rlogTransformation(DeResult[[3]]) )

zexllin/lncRNAtools documentation built on Jan. 1, 2021, 1:52 p.m.