Integrated microbial index
This package can be installed using devtools.
devtools::install_github('rusher321/metaindex@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)
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- Please report any issues or bugs.
- License: MIT
- Get citation information for
metaindexin R doingcitation(package = 'metaindex') - 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.