R/complexes_genes.R

In saezlab/OmnipathR: OmniPath web service client and more

#!/usr/bin/env Rscript

#
#  This file is part of the `OmnipathR` R package
#
#  Copyright
#  2018-2024
#  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
#
#  File author(s): Alberto Valdeolivas
#                  Dénes Türei (turei.denes@gmail.com)
#                  Attila Gábor
#
#  Distributed under the MIT (Expat) License.
#  See accompanying file `LICENSE` or find a copy at
#      https://directory.fsf.org/wiki/License:Expat
#
#  Website: https://r.omnipathdb.org/
#  Git repo: https://github.com/saezlab/OmnipathR
#


#' Get all the molecular complexes for a given gene(s)
#'
#' This function returns all the molecular complexes where an input set
#' of genes participate. User can choose to retrieve every complex where
#' any of the input genes participate or just retrieve these complexes where
#' all the genes in input set participate together.
#'
#' @param complexes complexes data frame (obtained using
#'     \code{\link{import_omnipath_complexes}})
#' @param select_genes vector containing the genes for whom complexes will be
#'     retrieved (hgnc format).
#' @param total_match [default=FALSE] logical indicating if the user wants to
#'     get all the complexes where any of the input genes participate (FALSE)
#'     or to get only the complexes where all the input genes participate
#'     together (TRUE).
#'
#' @export
#'
#' @return Data frame of complexes
#'
#' @examples
#' complexes <- import_omnipath_complexes(
#'     filter_databases = c("CORUM", "hu.MAP")
#' )
#' query_genes <- c("LMNA", "BANF1")
#' complexes_query_genes <- get_complex_genes(complexes, query_genes)
#'
#' @seealso \code{\link{import_omnipath_complexes}}
get_complex_genes <- function(
    complexes = import_omnipath_complexes(),
    select_genes,
    total_match = FALSE
){

    if(is.null(select_genes)){
        stop("A vector of genes should be provided")
    }

    if (!is.logical(total_match)){
        stop("total_match parameter should be logical")
    }

    if (total_match){
        complexes_geneset <-
        complexes[
            which(unlist(lapply(
                strsplit(complexes$components_genesymbols, '_'),
                function(x){
                    sum(x %in% select_genes) == length(select_genes)
                }
            ))),
        ]
    } else {
        complexes_geneset <-
        complexes[
            which(unlist(lapply(
                strsplit(complexes$components_genesymbols, '_'),
                function(x){any(x %in% select_genes)}
            ))),
        ]
    }

    return(complexes_geneset)
}