README.md

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.

TwoSLSanalysis

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

Installation

It is easy to install the development version of TwoSLSanalysis package using the 'devtools' package. The typical install time on a "normal" desktop computer is less than one minute.

# install.packages("devtools")
library(devtools)
install_github("LULIU1816/TwoSLSanalysis")

Usage

The main function is TwoSLSanalysis for two stage analysis of cancer (eg.Lung adenocarcinoma (LUAD)) individual level data downloaded from TCGA, other functions casecontrolfunction which has a 1:1 case-control gene expression data; edgeRfunction which performs a differentially expressed genes analysis required edgeR package; ChAMPfunction which performs a differentially methylated genes analysis required ChAMP package; selectmethysample, selectexpressionsample which selects the tumor and normal tissues in methylation and expression respectively; overlapaverage which averages the repeated measures data of LUAD methylation if exisit, and concrete analysis should be made according to concrete circumstance; clinicalfunction which performs clinical data such as transforming one type of data to another; stage1function which obtains predictions of the first stage with the advantage of fast computation and memory release. Moreover, you can find the instructions by '?TwoSLSanalysis','?casecontrolfunction' and so on.

library(TwoSLSanaylsis)

?TwoSLSanalysis

?casecontrolfunction

?edgeRfunction

?ChAMPfunction

?selectmethysample

?selectexpressionsample

?overlapaverage

?clinicalfunction

?stage1function

Example

#load required R packages

library("TwoSLSanalysis")

library("data.table")

library("edgeR")

library("ChAMP")

library("survival")

#read clinical data

clinical<-fread("nationwidechildrens.org_clinical_patient_lusc.txt",data.table=F,head=T)
clinical <- as.data.frame(clinical)[-c(1,2),]

#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)

#read methylation data

data_methy<-fread("LUSC__methylation_450__tissueTypeAll__20181024055604.txt",data.table=F,head=T)
data_methy <- as.data.frame(data_methy)[,-c(2,3,4)]

#configure path of GDC data

testDir = "~/GDCdata"

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


# Development
This R package is developed by Lu Liu.

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