getLigandsReceptors.Rd 2.73 KB
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/getLigandsReceptors.R
\name{getLigandsReceptors}
\alias{getLigandsReceptors}
\title{Retrieve a database of ligand-receptor pairs}
\usage{
getLigandsReceptors(version = "latest",
  cellularCompartment = c("Membrane", "ECM", "Both", "Secreted"),
  manualAnnotation = "Correct", ligandClass = c("Other", "Cytokine",
  "Chemokine", "GrowthFactor", "Interleukin"))
}
\arguments{
\item{version}{Currently supports the following values: \itemize{
  \item{latest} points to \code{1.0.0}
  \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.
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  \item{2.0.0} contains manual annotation for all genes in the geneome (not yet complete)
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  \item Alternatively, a data frame with the same column names as \code{ligandsReceptors_1.0.0} can be used.
}}

\item{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.}

\item{manualAnnotation}{A character vector to select permitted annotation status of the interaction. Valid entries are \code{Correct}, \code{Incorrect}, \code{Not Expressed} (i.e. entries not annotated in v1.0.0) and \code{Irrelevant} (i.e. entries we consider correct but not relevant at homeostasis, e.g. interactions involving activated components of the complement system)}

\item{ligandClass}{A character vector to select permitted classes of ligands. Defaults to all, i.e. \code{c("Other","Cytokine","Chemokine","GrowthFactor","Interleukin")}}
}
\value{
Returns a data frame with 11 columns: \itemize{
\item{Pair.Name}{Unique identifier for the ligand-receptor pair}
\item{Ligand.Mouse}{MGI symbol of the ligand. }
\item{Receptor.Mouse}{MGI symbol of the receptor. In case multiple receptors are required for complex formation, multiple MGI symbols separated by \strong{&}, as in Itgal&Itgb2. }
\item{Source}{Ramilowski for entries taken from \emph{Ramilowski et al., Nature Communications 2015}; Baccin for entries added as part of this work}
\item{Reference}{Pubmed ID or similar}
\item{ManualAnnotation}{The literature evidence for all entries from Ramilowski et al with expression in bone where checked manually.}
\item{Ligand.CC}{Cellular Compartment of the ligand - one of Secreted, Membrane, Both, or ECM. Annotation is based on Gene Ontology, but was checked manually for entries with expression in bone}
\item{Ligand.GO}{Classification of the ligand by gene ontology into one of the following classes: GrowthFactor, Cytokine, Chemokine, Interleukin, or Other}
}
}
\description{
Retrieve a database of ligand-receptor pairs
}