README.md

In pancor: Calculation and Plot of Gene Correlationship in TCGA/GTEx/CCLE

pancor

Installation

devtools::install_github("xuzhougeng/pancor")
library(pancor)

Usage:

test dasta

data("pancancer_small")
df <- pancor(pancancer_small, "METTL3", "SETD2")
ggpancor(df)

ggcorplot(pancancer_small, "METTL3","SETD2", cor.test.method = "pearson")

If you want to use the full data, you need download our preprocessed Rdata with getExprSet

getExprSet("pancancer_mRNA_exprSet.Rdata")

Then load this data to environment

load("pancancer_mRNA_exprSet.Rdata")

The following analysis is same as previous

df <- pancor(mRNA_exprSet, "METTL3", "SETD2")
ggpancor(df)

ggcorplot(mRNA_exprSet, "METTL3","SETD2", cor.test.method = "pearson")

Reference

• 跟Nature一起学习TCGA,GTEx和CCLE数据库的使用

pancor documentation built on Oct. 30, 2019, 10:04 a.m.