docs: further small adjustments

R/complexes_genes.R

@@ -39,9 +39,7 @@
 #' @return Data frame of complexes
 #'
 #' @examples
-#' complexes <- complexes(
-#'     filter_databases = c("CORUM", "hu.MAP")
-#' )
+#' complexes <- complexes(resources = c("CORUM", "hu.MAP"))
 #' query_genes <- c("LMNA", "BANF1")
 #' complexes_with_query_genes <- complex_genes(complexes, query_genes)
 #'

R/interactions.R

@@ -105,6 +105,7 @@ GRN_DATASETS <- c('dorothea', 'tf_target', 'collectri')
 #' }
 #'
 #' @name omnipath-interactions
+#' @md
 NULL
 
 
@@ -453,16 +454,7 @@ import_dorothea_interactions <- function(...){
 #' @export
 #' @rdname omnipath-interactions
 #' @aliases import_tf_target_interactions
-tf_target <- function(
-    resources = NULL,
-    organism = 'human',
-    fields = NULL,
-    default_fields = TRUE,
-    references_by_resource = TRUE,
-    exclude = NULL,
-    strict_evidences = FALSE,
-    ...
-){
+tf_target <- function(...){
 
     args <- omnipath_args(
         list(...),

R/omnipath.R

@@ -163,7 +163,7 @@ ORGANISMS_SUPPORTED <- c(9606L, 10090L, 10116L)
 #'     before returning the result.
 #' @param resources Character vector: name of one or more resources. Restrict
 #'     the data to these resources. For a complete list of available resources,
-#'     call the `get_<query_type>_resources` functions for the query type of
+#'     call the `<query_type>_resources` functions for the query type of
 #'     interst.
 #' @param datasets Character vector: name of one or more datasets. In the
 #'     interactions query type a number of datasets are available. The default