TwoSLSanalysis: TwoSLSanalysis

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

TwoSLSanylsis can provide the estimate of causal effect with the survival data download from TCGA.

Usage

TwoSLSanalysisLUAD(clinical,data_normalized,data_count,data_methy,testDir,fdr=0.001,logfc=2.5,logcpm=2.5,cores=1)

Examples

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

#read clinical data
clinical<-fread("nationwidechildrens.org_clinical_patient_luad.txt",data.table=F,head=T)
clinical <- as.data.frame(clinical)[-c(1,2),]
#read expression data
data_normalized<-fread("LUAD__gene.normalized_RNAseq__tissueTypeAll__20181022065043.txt",data.table=F,head=T)
data_count<-fread("LUAD__gene_RNAseq__tissueTypeAll__20181022065942.txt",data.table=F,head=T)
data_normalized <- as.data.frame(data_normalized)
data_count <-as.data.frame(data_count)
#read methylation data
data_methy<-fread("LUAD__methylation_450__tissueTypeAll__20181024043150.txt",data.table=F,head=T)
data_methy <- as.data.frame(data_methy)[,-c(2,3,4)]

#configure path of GDC data
testDir = "~/GDCdata"

LUADresult <-TwoSLSanalysis(clinical,data_normalized,data_count,data_methy,testDir)

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