README.md

In xlucpu/hccPIRS: Replication stress-related prognostic index in HCC

hccPIRS

Introduction

This package calculates replication stress-related prognostic index (PIRS) for HBV-associated HCC patients, and estimates the enrichment of 21 replication stress signatures. If specified, a heatmap will be generated to show the landscape of the replication stress signatures in an ascending order of PIRS score.

Citation

For now, you can cite the following bioRxiv preprint

Installation

You may install this package with:

if (!require("devtools")) 
    install.packages("devtools")
devtools::install_github("xlucpu/hccPIRS")

Example

## basic example code
library(hccPIRS)
load(system.file("extdata", "tpm.demo.RData", package = "hccPIRS", mustWork = TRUE)) # load example data

res <- hccPIRS(expr       = tpm.demo,
               scaleFlag  = FALSE, # no scale for input data
               centerFlag = FALSE, # no center for input data
               doplot     = TRUE, # generate heatmap
               fig.path   = getwd(),
               fig.name   = "heatmap of replication stress",
               enrich     = "gsva", # use gsva to quantify enrichment
               width      = 6,
               height     = 4)

pirs <- res$pirs # extract normalized PIRS score for each sample
print(pirs)

rsMat <- res$RS.score # extract enrichment score for replication stress signatures
rsMat[1:21,1:3]

res$hm # show the heatmap

xlucpu/hccPIRS documentation built on Dec. 23, 2021, 7:10 p.m.