Nothing
## ---- echo = FALSE, eval = TRUE-----------------------------------------------
websiteLive <- TRUE
## ---- echo = TRUE, eval = FALSE-----------------------------------------------
# library(devtools)
# install_github("wjawaid/enrichR")
## ---- echo = TRUE, eval = FALSE-----------------------------------------------
# install.packages("enrichR")
## ---- echo = TRUE, eval = TRUE------------------------------------------------
library(enrichR)
websiteLive <- getOption("enrichR.live")
if (websiteLive) {
listEnrichrSites()
setEnrichrSite("Enrichr") # Human genes
}
## ---- echo = TRUE, eval = TRUE------------------------------------------------
if (websiteLive) dbs <- listEnrichrDbs()
## ---- echo = TRUE, eval = TRUE------------------------------------------------
## if (is.null(dbs)) websiteLive <- FALSE
if (websiteLive) head(dbs)
## ---- echo = FALSE, results='asis'--------------------------------------------
library(knitr)
if (websiteLive) kable(head(dbs[c(1:6),-4]))
## ---- echo = TRUE, eval = TRUE------------------------------------------------
dbs <- c("GO_Molecular_Function_2015", "GO_Cellular_Component_2015", "GO_Biological_Process_2015")
if (websiteLive) {
enriched <- enrichr(c("Runx1", "Gfi1", "Gfi1b", "Spi1", "Gata1", "Kdr"), dbs)
}
## ---- echo = TRUE, eval = FALSE-----------------------------------------------
# if (websiteLive) enriched[["GO_Biological_Process_2015"]]
## ---- echo = FALSE, results = 'asis'------------------------------------------
success <- ifelse(exists("enriched"), TRUE, FALSE) & websiteLive
success <- success & (length(enriched) >= 3)
success <- success & all(dim(enriched[[3]]) > 2)
if (success) {
x <- head(enriched[["GO_Biological_Process_2015"]])
x[,1] <- gsub("GO:", "GO_", x[,1])
kable(x)
}
## ---- echo = TRUE, eval = TRUE, fig.width = 8, fig.height = 6, fig.align = "center", dpi = 100----
if (websiteLive) {
plotEnrich(enriched[[3]], showTerms = 20, numChar = 40, y = "Count", orderBy = "P.value")
}
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