Commit 50b73284 authored by Lars Velten's avatar Lars Velten
Browse files

closed a bracket

parent fe55fa26
......@@ -65,7 +65,7 @@ RNAMagnetSignaling <- function(seurat, neighborhood.distance = NULL, neighborhoo
#'@param .k Fuzzification parameter, see detail. Recommended to leave at the default value.
#'@param .x0 Fuzzification parameter, see detail. Recommended to leave at the default value.
#'@param .minExpression Minimal expression level of genes to be included, specified as the number of cells in the dataset that express the gene.
#'@param .version The version of the underlying ligand-receptor database. Recommended to leave at the default value. See \code{\link{getLigandsReceptors}}.
#'@param .version The version of the underlying ligand-receptor database. See \code{\link{getLigandsReceptors}}.
#'@param .cellularCompartment Types of ligands to be included. For physical interactions, defaults to \code{ c("Membrane","ECM","Both")}. See \code{\link{getLigandsReceptors}}.
#'@param .manualAnnotation Annotation status of ligands to be included. Default to \code{"Correct"}. See \code{\link{getLigandsReceptors}}.
#'@param .symmetric Assume that if A is a receptor for B, B is also a receptor for A
......
#'Retrieve a database of ligand-receptor pairs
#'
#'@param version Currently supports the following values: \itemize{
#' \item{latest} points to \code{2.1.0}
#' \item{stable} points to \code{1.0.0}
#' \item{latest} points to \code{2.2.0}
#' \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, January 2019
#' \item{2.1.0} integrates heterodimer information for non-integrin receptors from cellphoneDB., Janary 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{3.0.0} adds a translation of the complete cellphoneDB to mouse homologues.
#' \item Alternatively, a data frame with the same column names as \code{ligandsReceptors_1.0.0} can be used.
#'}
#'@param cellularCompartment A character vector to select permitted localizations of the \strong{ligand}. Valid entries are \code{Membrane}, \code{ECM}, \code{Secreted} and \code{Both}, which refers to membrane-bound ligands that can also be secreted.
......@@ -26,6 +27,7 @@
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_2.2.0,
stable = ligandsReceptors_1.0.0,
"1.0.0" = ligandsReceptors_1.0.0,
"2.0.0" = ligandsReceptors_2.0.0,
"2.1.0" = ligandsReceptors_2.1.0,
......
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