Commit b2fb32a7 authored by Lars Velten's avatar Lars Velten
Browse files

added database v.2.2.0

parent 2164d32e
......@@ -3,8 +3,9 @@
#'@param version Currently supports the following values: \itemize{
#' \item{latest} points to \code{2.1.0}
#' \item{1.0.0} contains manual annotation for all genes expressed in bone marrow. This version was used for analysis is the Baccin et al paper. Information on heterodimeric receptors is only included for integrins.
#' \item{2.0.0} contains manual annotation for all genes in the geneome (not yet complete).
#' \item{2.1.0} integrates heterodimer information for non-integrin receptors from cellphoneDB.
#' \item{2.0.0} contains manual annotation for all genes in the geneome, January 2019
#' \item{2.1.0} integrates heterodimer information for non-integrin receptors from cellphoneDB., Janary 2019
#' \item{2.2.0} updated to remove missing entries and several additions, April 2019
#' \item{3.0.0} adds a translation of the complete cellphoneDB to mouse homologues (not tested).
#' \item Alternatively, a data frame with the same column names as \code{ligandsReceptors_1.0.0} can be used.
#'}
......@@ -24,10 +25,11 @@
#'@export
getLigandsReceptors <- function(version = "latest", cellularCompartment = c("Membrane","ECM","Both","Secreted"), manualAnnotation = "Correct", ligandClass = c("Other","Cytokine","Chemokine","GrowthFactor","Interleukin")) {
if (is.character(version)) out <- switch(version,
latest = ligandsReceptors_2.1.0,
latest = ligandsReceptors_2.2.0,
"1.0.0" = ligandsReceptors_1.0.0,
"2.0.0" = ligandsReceptors_2.0.0,
"2.1.0" = ligandsReceptors_2.1.0,
"2.2.0" = ligandsReceptors_2.2.0,
"3.0.0" = ligandsReceptors_3.0.0) else if (is.data.frame(version)) out <- version else stop("Version needs to be a character string or a data frame.")
if(is.null(out)) error("Version", version, "not supported. See documentation.")
......
......@@ -2,7 +2,7 @@ To install from within R, you can use the `install_git` function from the `devto
```
install.packages("devtools")
devtools::install_git("https://git.embl.de/velten/STEMNET/")
devtools::install_git("https://git.embl.de/velten/rnamagnet/")
```
In case this fails, download the tar.gz archive, unpack to a directory of your choice (e.g. /path/to) and inside R run
......
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