README.md

In onesand1/GRC: Gene regulation and correlation between target and pathway

GRC

A R package for gene Interrelation and correlation analysis

title: "example" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{example} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}

```{r, include = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )

```{r downstream}
library(GRC)

data=system.file("data","data.Rda", package="GRC")
load(data) 
gene="100134869"
res=regulator(gene,data)
plot.reg.down(res,type="circle")

```{r upstream} gene="100134869" res=regulator(gene,data,type=2) res=Top(res,10) plot.reg.up(res,type="circle")

```{r The correlation between gene expression and pathway score }
 gg=list(TEST=res$target[c(1:12)])
GP(data,gg)

```{r Synthetic lethal analysis} load('data.Rda') #This data included in GRC package root or data directory. data=t(data) data=data[,1] mutation=rep(c(2,1,0),c(20,18,7)) sample=rownames(data) data=cbind(sample,data) data=cbind(data,mutation)

colnames(data)=c('sample','expression','group') SL(data=data,plot = FALSE)

```{r}
library(survival)
library(GRC)
library(survminer)
library(survivalROC)
data(lung)
n=dim(lung)[1]
data=cbind(lung$age,lung$time)
data=cbind(data,lung$status)
cutoff(data,type = "Y")

onesand1/GRC documentation built on Dec. 22, 2020, 1:38 a.m.