oma_pairwise_genesymbols: convenient wrapper to get pairwase orthol…

…ogous gene table with gene symbols (related to saezlab/liana#137)

NAMESPACE

@@ -169,6 +169,7 @@ export(obo_parser)
 export(oma_code)
 export(oma_organisms)
 export(oma_pairwise)
+export(oma_pairwise_genesymbols)
 export(omnipath)
 export(omnipath_cache_autoclean)
 export(omnipath_cache_clean)

R/id_mapping.R

@@ -396,6 +396,7 @@ translate_ids <- function(
         .nse_ensure_str(!!enquo(organism)) %>%
         {`if`(. == 'organism', organism, .)} %>%
         ncbi_taxid
+
     id_cols <- names(ids)
     id_types <- unlist(ids)
     from_col <- id_cols[1]

R/oma.R

@@ -153,6 +153,67 @@ oma_pairwise <- function(
 }
 
 
+#' Orthologous pairs of gene symbols between two organisms
+#'
+#' The Orthologous Matrix (OMA), a resource of orthologous relationships
+#' between genes, doesn't provide gene symbols, the identifier preferred in
+#' many bioinformatics pipelines. Hence this function wraps
+#' \code{\link{oma_pairwise}} by translating the identifiers used in OMA to
+#' gene symbols. Items that can not be translated to `id_type` (but present
+#' in the data with their internal OMA IDs) will be removed. This part is done by . Then,
+#' in this function we translate the identifiers to gene symbols.
+#'
+#' @param organism_a Name or identifier of an organism.
+#' @param organism_b Name or identifier of another organism.
+#' @param id_type The gene or protein identifier to use in the table. For a
+#'     list of supported ID types see `omnipath.env$id_types$oma`. These are
+#'     the identifiers that will be translated to gene symbols.
+#' @param mappings Character vector: control ambiguous mappings: \itemize{
+#'         \item{1:1 - unambiguous}
+#'         \item{1:m - one-to-many}
+#'         \item{n:1 - many-to-one}
+#'         \item{n:m - many-to-many}
+#'     }
+#' @param only_ids Logical: include only the two identifier columns, not the
+#'     mapping type and the orthology group columns.
+#'
+#' @return A data frame with orthologous gene pairs.
+#'
+#' @examples
+#' oma_pairwise_genesmybols("human", "mouse")
+#'
+#' @importFrom magrittr %>%
+#' @importFrom rlang exec !!! !! := sym
+#' @importFrom dplyr filter
+#' @export
+oma_pairwise_genesymbols <- function(
+    organism_a = 'human',
+    organism_b = 'mouse',
+    id_type = 'uniprot',
+    mappings = c('1:1', '1:m', 'n:1', 'n:m'),
+    only_ids = TRUE
+) {
+
+    .slow_doctest()
+
+    environment() %>%
+    as.list %>%
+    exec(oma_pairwise, !!!.) %>%
+    translate_ids(
+        id_organism_a := !!sym(id_type),
+        id_organism_a := genesymbol,
+        organism = !!sym(organism_a)
+    ) %>%
+    translate_ids(
+        id_organism_b := !!sym(id_type),
+        id_organism_b := genesymbol,
+        organism = !!sym(organism_b)
+    ) %>%
+    filter(!is.na(id_organism_a) & !is.na(id_organism_b))
+
+}
+
+
 #' OMA identifier type from synonyms and lower case version
 #'
 #' @param id_type Character: a synonym or a lower case version of an OMA