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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# LPRI
<!-- badges: start -->
<!-- badges: end -->
“LuProgRegu Index” (LPRI) is an algorithm to calculate an index to help lung cancer patients’ prognostic stratification from regulons
![workflow.png](https://github.com/Richard-Li-lab-team/LPRI/blob/master/img/workflow.jpg?raw=true)
## Installation
You can install the development version from [GitHub](https://github.com/) with:
```
# install.packages("devtools")
devtools::install_github("Richard-Li-lab-team/LPRI")
```
```{r}
if (!require("GSVA")) BiocManager::install("GSVA")
```
## Example
```{r}
library(LPRI)
library(dplyr)
```
### load data
```{r}
# load data required for calculate the LPRI score
load(paste0(system.file("extdata", package = "LPRI"),"/sysdata.rda"))
```
```{r}
# load gene expression profile and you can prepare you own
# here is the example data
load(paste0(system.file("extdata", package = "LPRI"),"/genes_expr.rda"))
genes_expr[1:5,1:5]
```
### Run LPRI with one line
```{r}
Sample_risk <- runLPRI(genes_expr)
```
```{r}
head(Sample_risk)
```
## Citation
Please cite:
Yi Xiong, Yihao Zhang et al., Integration of single-cell regulon atlas and multi-omics data for prognostic stratification and personalized treatment prediction in human lung adenocarcinoma (Manuscript in submission)