edgeRfunction: edgeRfunction

In LULIU1816/TwoSLSanalysis: TwoSLSanylsis is an two-stage least squares procedure for TCGA analysis. TwoSLSanylsis can provide the estimate of causal effect with the survival data download from TCGA.

Description

perform a differentially expressed genes analysis required edgeR package

Usage

edgeRfunction(case_control_data,fdr=0.001,logfc=2.5,logcpm=2.5)

Examples

library("data.table")
library("edgeR")

#read expression data 
data_normalized<-fread("LUSC__gene.normalized_RNAseq__tissueTypeAll__20181022104424.txt",data.table=F,head=T) 
data_count<-fread("LUSC__gene_RNAseq__tissueTypeAll__20181022105257.txt",data.table=F,head=T) 
data_normalized <- as.data.frame(data_normalized) 
data_count <-as.data.frame(data_count)

# structure case-control data
case_control_data <- casecontrolfunction(data_count,data_tumor)

# edgeR
diff_gene_edgeR <- edgeRfunction(case_control_data)
diff_gene <- diff_gene_edgeR[,1]

LULIU1816/TwoSLSanalysis documentation built on Nov. 18, 2019, 5:41 a.m.