Nothing
#' getCPX
#' @title Fetch Complexes from the CORUM Database
#' @param org Mammalian model organisms including: "Human", "Mouse",
#' "Pig", "Bovine", "Rat", "Mammalia", "Rabbit", "Dog", "Hamster",
#' and "MINK". Defaults to "Mouse".
#' @param tpath A character string indicating the path to the project
#' directory. If the directory is
#' missing, it will be stored in the temp directory.
#' @return A list containing protein complexes for mammalian organisms.
#' @author Matineh Rahmatbakhsh, \email{matinerb.94@gmail.com}
#' @importFrom utils read.delim
#' @importFrom utils download.file
#' @importFrom utils unzip
#' @importFrom dplyr filter
#' @description This function retrieves protein complexes directly from the
#' CORUM database.
#' @export
getCPX <- function(org = "Mouse",
tpath = tempdir()) {
Organism <- NULL
url <-
"http://mips.helmholtz-muenchen.de/corum/download"
query <-
paste0(url, "/","coreComplexes.txt.zip")
temp <- tempfile()
# Download the file
download.file(query,temp)
# Extract the target file from temp
RawFile <- read.delim(unzip(file.path(temp)))
file.remove("coreComplexes.txt")
# Extract the cpx for specific organism
RawFile <-
filter(RawFile, Organism %in% org)
# Extract cpx with >= 3 members
rawCpx <-
strsplit(RawFile[, 6], ";")
names(rawCpx) <-
RawFile[, 2]
CORUMcpx <-
rawCpx[unlist(lapply(rawCpx, length)) >= 3]
fname <- file.path(tpath, "CORUMcpx.rda")
save(CORUMcpx, file = fname)
return(CORUMcpx)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.