The goal of ReportScore is to compute the reportscore of pathway or module
This package can be installed using devtools.
devtools::install_github('rusher321/ReportScore@master')This is a basic example which shows you how to solve a common problem:
library(ReportScore)
## basic example code
pr <- read.table("testdata/all.KEGG.abun.txt",row.names = 1,header = T,sep = "\t")
grp <- read.table("testdata/sampleinfo.txt",row.names = 1,header = T,sep = "\t")
grp_sub <- grp[which(grp$TimePoint == "Day2"), 1, drop=F]
grp_sub$Protein <- ifelse(grp_sub$Protein == "C-Pork", "B-Beef", grp_sub$Protein)
pr_sub <- pr[, rownames(grp_sub)]
res_D2 <- ReporterScore(pr_sub, grp_sub, paired = F, database = "./database", occ = 0.1)
fig <- ReportVis(res_D2, color = c("#2470a0", "#DE3C3C"), exclude = T)
## if you want update the datebase
download_data(db_dir = "database/")
## if you want plot the output
fig <- ReportVis(res, color = c("#2470a0", "#DE3C3C"), exclude = T)
the test.R have real data can to test,the output like
We welcome comments, criticisms, and especially contributions! GitHub issues are the preferred way to report bugs, ask questions, or request new features. You can submit issues here:
https://github.com/rusher321/ReportScore/issues
- [√]Visualization of reportscore result
- [ ]parallel compute of multi group
- Please report any issues or bugs.
- License: MIT
- Get citation information for
ReportScorein R doingcitation(package = 'ReportScore') - Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.