DEGs: Performe differential expression analysis

In leiming8886/fRNC: ncRNA module search functions

Performe differential expression analysis

Description

Differential expression analysis using edgeR or limma for two group comparison

Usage

DEGs(case.exp, control.exp, geneid, data_type)

Arguments

case.exp	the case expression matrix, in which the row name is gene id and the column name is sample id
control.exp	the control expression matrix, in which the row name is gene id (the same with the case) and the column name is sample id
geneid	gene id in the case or control expression matrix
data_type	a character string indicating which date type to deal with is to be choosed, One of "RNAseq_counts" , "fpkm" and "microarray": can be abbreviated

Value

DEGlist contain four elements, DEGs the differential expression matrix, Nor_expr the normalized expression matrix, data_type a character string of the data type algorithm a character string indicating which algorithm was used, One of "edgeR" , "limma"

Examples

## Not run: 
data("case.exp_miRNA")
data("control.exp_miRNA")
result_miR <- DEGs(case.exp_miRNA,control.exp_miRNA,
geneid= rownames(control.exp_miRNA), data_type = "RNAseq_counts")


## End(Not run)

leiming8886/fRNC documentation built on Feb. 21, 2023, 4:12 p.m.