177 improve annotation mapping through readgmt

NAMESPACE

@@ -79,6 +79,7 @@ importFrom(SingleCellExperiment,SingleCellExperiment)
 importFrom(SpatialExperiment,SpatialExperiment)
 importFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(SummarizedExperiment,assay)
+importFrom(cli,cli_abort)
 importFrom(cli,cli_alert_info)
 importFrom(cli,cli_alert_success)
 importFrom(cli,cli_alert_warning)

R/GSVA-package.R

@@ -33,4 +33,5 @@
 #' currentBlockId read_block gridReduce write_block close t colSums
 #' @importFrom HDF5Array HDF5RealizationSink writeHDF5Array
 #' @importFrom BiocSingular runRandomSVD
+#' @importFrom cli cli_abort cli_alert_info cli_alert_warning cli_alert_success
 NULL

R/gsvaNewAPI.R

@@ -863,9 +863,8 @@ geneIdsToGeneSetCollection <- function(geneIdsList,
 #' @description Imports a list of gene sets from a GMT (Gene Matrix Transposed)
 #' format file, offering a choice of ways to handle duplicated gene set names.
 #' 
-#' @param con A connection object or character string containing e.g.
-#' the file name or URL of a GTM file.  This is directly passed to [`readLines`]
-#' and hence may contain anything that `readLines()` can handle.
+#' @param con A connection object or a non-empty character string of length 1
+#' containing e.g. the filename or URL of a (possibly compressed) GMT file. 
 #'
 #' @param sep The character string separating members of each gene set in the
 #' GMT file.
@@ -919,6 +918,28 @@ geneIdsToGeneSetCollection <- function(geneIdsList,
 #' 
 #' @seealso [`readLines`], [`GeneSetCollection`], [`getGmt`]
 #'
+#' @examples
+#' library(GSVA)
+#' library(GSVAdata)
+#'
+#' fname <- system.file("extdata", "c7.immunesigdb.v2024.1.Hs.symbols.gmt.gz",
+#'                      package="GSVAdata")
+#'
+#' ## by default, guess geneIdType from content and return a GeneSetCollection
+#' genesets <- readGMT(fname)
+#' genesets
+#'
+#' ## how to manually override the geneIdType
+#' genesets <- readGMT(fname, geneIdType=NullIdentifier())
+#' genesets
+#' 
+#' ## return a simple list instead of a GeneSetCollection
+#' genesets <- readGMT(fname, valueType="list")
+#' head(genesets, 2)
+#'
+#' ## the list has a geneIdType, too
+#' gsvaAnnotation(genesets)
+#'
 #' @aliases readGMT
 #' @name readGMT
 #' @rdname readGMT
@@ -932,6 +953,10 @@ readGMT <- function (con,
                      deduplUse = c("first", "drop", "union", "smallest", "largest"),
                      ...) {
     valueType <- match.arg(valueType)
+
+    if((!.isCharLength1(con)) && (!inherits(con, "connection"))) {
+        cli_abort("Argument 'con' is not a valid filename, URL or connection.")
+    }
 
     ## from GSEABase::getGmt()
     lines <- strsplit(readLines(con, ...), sep)