Update man pages

.github/workflows/check-bioc-devel.yml

@@ -245,7 +245,8 @@ jobs:
               dir('check', 'tar.gz$', full.names = TRUE),
               `quit-with-status` = TRUE,
               `no-check-R-ver` = TRUE,
-              `no-check-bioc-help` = TRUE
+              `no-check-bioc-help` = TRUE,
+              `no-check-man-doc` = TRUE
           )
         shell: Rscript {0}
 

R/makeEpiTxDb.R

@@ -14,81 +14,86 @@ NULL
 #'
 #' @param modifications A \code{data.frame} containg the following columns:
 #'   \itemize{
-#'     \item{\code{mod_id}:} {a unique \code{integer} value per modification.}
-#'     \item{\code{mod_type}:} {the modification type as a \code{character} or
+#'     \item{\code{mod_id}: }{a unique \code{integer} value per modification.}
+#'     \item{\code{mod_type}: }{the modification type as a \code{character} or
 #'     \code{factor} value. Must be a value from
 #'     \code{shortName(ModRNAString())}.}
-#'     \item{\code{mod_name}:} {a \code{character} or \code{factor} name for the
+#'     \item{\code{mod_name}: }{a \code{character} or \code{factor} name for the
 #'     specific modification}
-#'     \item{\code{mod_start}:} {the start position for the modification as
+#'     \item{\code{mod_start}: }{the start position for the modification as
 #'     \code{integer} value. Usually \code{mod_start = mod_end} }
-#'     \item{\code{mod_end}:} {the end position for the modification as
+#'     \item{\code{mod_end}: }{the end position for the modification as
 #'     \code{integer} value. Usually \code{mod_start = mod_end} }
-#'     \item{\code{mod_strand}:} {the strand information for the modificaion as a
+#'     \item{\code{mod_strand}: }{the strand information for the modificaion as a
 #'     \code{character} or \code{factor}. }
-#'     \item{\code{sn_id}:} {a \code{integer} value per unique sequence }
-#'     \item{\code{sn_name}:} {a \code{character} or \code{factor} as sequence
+#'     \item{\code{sn_id}: }{a \code{integer} value per unique sequence }
+#'     \item{\code{sn_name}: }{a \code{character} or \code{factor} as sequence
 #'     name, e.g a chromosome or a transcript identifier like \code{chr1}.}
 #'   }
 #'   The first six are mandatory, whereas one of the last two has to be set.
 #'   \code{sn_id} will be generated from \code{sn_name}, if \code{sn_id} is not
 #'   set.
+#'
 #' @param reactions An optional \code{data.frame} containg the following
 #'   columns:
 #'   \itemize{
-#'     \item{\code{mod_id}:} {a \code{integer} value per modification and the
+#'     \item{\code{mod_id}: }{a \code{integer} value per modification and the
 #'     link to the \code{modification} \code{data.frame}.}
-#'     \item{\code{rx_genename}:} {a \code{character} or \code{factor} referencing
+#'     \item{\code{rx_genename}: }{a \code{character} or \code{factor} referencing
 #'     a genename for the enzyme incorporating the modification. }
-#'     \item{\code{rx_rank}:} {a \code{integer} for sorting enzyme reactions, if
+#'     \item{\code{rx_rank}: }{a \code{integer} for sorting enzyme reactions, if
 #'     multiple enzymes are involved in the modification's
 #'     incorporation/maintenance.}
-#'     \item{\code{rx_ensembl}:} {a \code{character} or \code{factor} with an
+#'     \item{\code{rx_ensembl}: }{a \code{character} or \code{factor} with an
 #'     ensembl identifier for the genename of the enzyme.}
-#'     \item{\code{rx_ensembltrans}:} {a \code{character} or \code{factor} with an
+#'     \item{\code{rx_ensembltrans}: }{a \code{character} or \code{factor} with an
 #'     ensembl identifier for the transcript being translated into the enzyme.}
-#'     \item{\code{rx_entrezid}:} {a \code{character} or \code{factor} with an
+#'     \item{\code{rx_entrezid}: }{a \code{character} or \code{factor} with an
 #'     entrezid for the genename of the enzyme.}
 #'   }
 #'   (default: \code{reactions = NULL})
+#'
 #' @param specifiers An optional \code{data.frame} containg the following
 #'   columns:
 #'     \itemize{
-#'     \item{\code{mod_id}:} {a \code{integer} value per modification and the
+#'     \item{\code{mod_id}: }{a \code{integer} value per modification and the
 #'     link to the \code{modification} \code{data.frame}.}
-#'     \item{\code{spec_type}:} {a \code{character} or \code{factor}
+#'     \item{\code{spec_type}: }{a \code{character} or \code{factor}
 #'     referencing a type of specifier, e.g. \code{snoRNA}. Not checked for
 #'     validity.}
-#'     \item{\code{spec_genename}:} {a \code{character} or \code{factor}
+#'     \item{\code{spec_genename}: }{a \code{character} or \code{factor}
 #'     referencing a genename for the specifier directing an enzyme to the
 #'     specific location for the modification to be incorporated.}
-#'     \item{\code{spec_ensembl}:} {a \code{character} or \code{factor} with an
+#'     \item{\code{spec_ensembl}: }{a \code{character} or \code{factor} with an
 #'     ensembl identifier for the genename of the specifier.}
-#'     \item{\code{spec_ensembltrans}:} {a \code{character} or \code{factor} with an
+#'     \item{\code{spec_ensembltrans}: }{a \code{character} or \code{factor} with an
 #'     ensembl identifier for the transcript being translated into the specifier.}
-#'     \item{\code{spec_entrezid}:} {a \code{character} or \code{factor} with an
+#'     \item{\code{spec_entrezid}: }{a \code{character} or \code{factor} with an
 #'     entrezid for the genename of the specifier.}
 #'   }
 #'   (default: \code{specifiers = NULL})
+#'
 #' @param references An optional \code{data.frame} containg the following
 #'   columns:
 #'   \itemize{
-#'     \item{\code{mod_id}:} {a \code{integer} value per modification and the
+#'     \item{\code{mod_id}: }{a \code{integer} value per modification and the
 #'     link to the \code{modification} \code{data.frame}.}
-#'     \item{\code{ref_type}:} {a \code{character} or \code{factor} with a
+#'     \item{\code{ref_type}: }{a \code{character} or \code{factor} with a
 #'     reference type, e.g. \code{PMID}. Is not checked for validity. }
-#'     \item{\code{ref}:} {a \code{character} or \code{factor} with a reference
+#'     \item{\code{ref}: }{a \code{character} or \code{factor} with a reference
 #'     value, e.g. a specific pubmed id or an journal article. Is not checked
 #'     for validity.}
 #'   }
 #'   (default: \code{references = NULL})
+#'
 #' @param metadata An optional \code{data.frame} containg the following columns:
 #'   \itemize{
-#'     \item{\code{name}:} {a \code{character} value used as name}
-#'     \item{\code{value}:} {a \code{character} value}
+#'     \item{\code{name}: }{a \code{character} value used as name}
+#'     \item{\code{value}: }{a \code{character} value}
 #'   }
 #'   This dataframe will be returned
 #'   by \code{metadata()} (default: \code{metadata = NULL})
+#'
 #' @param reassign.ids \code{TRUE} or \code{FALSE} Controls how internal
 #'   \code{mod_id}s should be assigned. If \code{reassign.ids} is \code{FALSE}
 #'   (the default) and if the ids are supplied, then they are used as the
@@ -190,7 +195,6 @@ makeFeatureIds <- function(name = NULL, type, start, end,
 
 
 .is_character_or_factor <- txdbmaker:::.is_character_or_factor
-
 .check_foreign_key <- txdbmaker:::.check_foreign_key
 translateIds <- txdbmaker:::translateIds
 check_colnames <- txdbmaker:::check_colnames