.Rhistory

library(devtools)
document()
document()
build()
check()
source('~/Documents/R/NACC/phiclust/R/phiclust.R', echo=TRUE)
source('~/Documents/R/NACC/phiclust/R/plot_g_phiclust.R', echo=TRUE)
data("out")
library(splatter)
data("splatO")
table(splatO$Group)
expr <- counts(splatO)
expr <- expr[rowSums(expr)>0,]
expr.norm <- t(t(expr)/colSums(expr))*10000
expr.norm.log <- log(expr.norm + 1)
test.cluster <- as.character(splatO$Group)
test.cluster[test.cluster == "Group3"] <- "Group2"
test.cluster[test.cluster == "Group4"] <- "Group2"
out <- phiclust(expr = expr.norm.log, clusters = test.cluster,
exclude = data.frame(clsm = log(colSums(expr) + 1)))
save(out, file = "data/out.rda")
document()
document()
document()
check()
devtools::install_github("semraulab/phiclust")
library(phiclust)
library(markdown)
render("vignettes/Guide_to_phiclust.Rmd", md_document(variant = "markdown_github")
)
library(rmarkdown)
render("vignettes/Guide_to_phiclust.Rmd", md_document(variant = "markdown_github"))
render("vignettes/Analysis_kidney.Rmd", md_document(variant = "markdown_github"))
render("vignettes/Guide_to_phiclust.Rmd", md_document(variant = "markdown_github"))
render("vignettes/Analysis_kidney.Rmd", md_document(variant = "markdown_github"))