Nothing
## ---- echo = FALSE, message = FALSE---------------------------------------------------------------
library(markdown)
options(markdown.HTML.options = c("use_xhtml", "smartypants", "base64_images", "mathjax", "highlight_code"))
options(markdown.HTML.stylesheet = system.file("resources", "markdown.css", package = "markdown"))
library(knitr)
knitr::opts_chunk$set(
error = FALSE,
tidy = FALSE,
message = FALSE,
warning = FALSE,
fig.align = "center")
options(width = 100)
options(rmarkdown.html_vignette.check_title = FALSE)
library(cola)
## ---- results = "hide"----------------------------------------------------------------------------
download.file("https://jokergoo.github.io/cola_examples/TCGA_GBM/TCGA_GBM_subgroup.rds",
destfile = "TCGA_GBM_subgroup.rds", quiet = TRUE)
rl = readRDS("TCGA_GBM_subgroup.rds")
file.remove("TCGA_GBM_subgroup.rds")
## -------------------------------------------------------------------------------------------------
library(cola)
res = rl["ATC:skmeans"]
res
## ---- fig.width = 8, fig.height = 7, out.width = "500"--------------------------------------------
set.seed(123)
get_signatures(res, k = 4)
## -------------------------------------------------------------------------------------------------
head(rownames(res))
## ---- eval = FALSE--------------------------------------------------------------------------------
# lt = functional_enrichment(res, k = 4)
## ---- echo = FALSE--------------------------------------------------------------------------------
if(file.exists("lt_functional_enrichment_TCGA_GBM.rds")) {
lt = readRDS("lt_functional_enrichment_TCGA_GBM.rds")
} else {
lt = functional_enrichment(res, k = 4)
saveRDS(lt, "lt_functional_enrichment_TCGA_GBM.rds", compress = "xz")
}
## -------------------------------------------------------------------------------------------------
names(lt)
head(lt[[1]])
## -------------------------------------------------------------------------------------------------
data(golub_cola)
## ---- fig.width = 8, fig.height = 7, out.width = "500"--------------------------------------------
res = golub_cola["ATC:skmeans"]
head(rownames(res))
set.seed(123)
get_signatures(res, k = 3)
## -------------------------------------------------------------------------------------------------
library(hu6800.db)
x = hu6800ENTREZID
mapped_probes = mappedkeys(x)
id_mapping = unlist(as.list(x[mapped_probes]))
head(id_mapping)
## -------------------------------------------------------------------------------------------------
sum(!is.na(id_mapping[rownames(res)]))/nrow(res)
## ---- eval = FALSE--------------------------------------------------------------------------------
# lt = functional_enrichment(res, k = 3, id_mapping = id_mapping)
## -------------------------------------------------------------------------------------------------
sessionInfo()
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