Browse code

small bugfixes

FelixErnst authored on 25/11/2019 23:05:39
Showing6 changed files

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@@ -791,11 +791,9 @@ setReplaceMethod(f = "settings",
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   # search for modifications
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   if(settings(ans,"find.mod")){
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     if(seqtype(ans) == seqtype(RNAString())){
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-      f <- which(Modstrings::shortName(Modstrings::ModRNAString()) %in% modType(ans))
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-      modName <- Modstrings::fullName(Modstrings::ModRNAString())[f]
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+      modName <- .get_modification_full_name(ans,seqtype(ans))
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     } else if(seqtype(ans) == seqtype(DNAString())){
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-      f <- which(Modstrings::shortName(Modstrings::ModDNAString()) %in% modType(ans))
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-      modName <- Modstrings::fullName(Modstrings::ModDNAString())[f]
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+      modName <- .get_modification_full_name(ans,seqtype(ans))
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     } else {
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       stop("")
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     }
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@@ -31,9 +31,10 @@ NULL
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 #' @param coord coordinates of position to subset to. Either a \code{GRanges} or
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 #' a \code{GRangesList} object. For both types the 'Parent' column is expected to
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 #' match the transcript name.
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-#' @param ... optional parameters:
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+#' @param name Optional: Limit results to one specific transcript.
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+#' @param pos Optional: Limit results to a specific position.
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+#' @param ... Optional parameters:
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 #' \itemize{
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-#' \item{\code{name}:} {Limit results to one specific transcript.}
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 #' \item{\code{type}:} {the modification type used for subsetting. By default 
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 #' this is derived from the \code{modType(x)}, but it can be overwritten using 
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 #' \code{type}. It must be a valid shortName for a modification according to
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@@ -55,11 +56,11 @@ NULL
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 #' If 'x' is a
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 #' \itemize{
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 #' \item{\code{\link[=SequenceData-class]{SequenceData}} or 
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-#' \code{\link[=Modifier-class]{Modifier}}} {a \code{SplitDataFrameList}
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+#' \code{\link[=Modifier-class]{Modifier}}:} {a \code{SplitDataFrameList}
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 #' with elments per transcript.}
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 #' \item{\code{\link[=SequenceDataSet-class]{SequenceDataSet}},
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 #' \code{\link[=SequenceDataList-class]{SequenceDataList}} or
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-#' \code{\link[=ModifierSet-class]{ModifierSet}}} {a \code{SimpleList} of
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+#' \code{\link[=ModifierSet-class]{ModifierSet}}:} {a \code{SimpleList} of
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 #' \code{SplitDataFrameList} with elments per transcript.}
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 #' }
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 #' 
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@@ -110,8 +111,7 @@ NULL
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   }
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 }
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-#' @rdname subsetByCoord
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-#' @export
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+#' @keywords internal
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 setMethod("subset",
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           signature = c(x = "Modifier"),
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           function(x, name, pos = 1L, ...){
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@@ -283,6 +283,8 @@ NULL
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   coord
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 }
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+#' @rdname subsetByCoord
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+#' @export
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 setMethod("subsetByCoord",
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           signature = c(x = "SplitDataFrameList", coord = "GRanges"),
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           function(x, coord, ...){
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@@ -448,8 +450,7 @@ setMethod("subsetByCoord",
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   .keep_one_labels_column(ans)
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 }
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-#' @rdname subsetByCoord
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-#' @export
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+#' @keywords internal
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 setMethod("labelByCoord",
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           signature = c(x = "SplitDataFrameList", coord = "GRanges"),
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           function(x, coord, ...){
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@@ -1,6 +1,14 @@
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 #' @include RNAmodR.R
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 NULL
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+.get_modification_full_name <- function(x, type = c("RNA","DNA")){
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+  type <- match.arg(type)
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+  className <- paste0("Mod",type)
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+  f <- which(Modstrings::shortName(Biostrings:::XString(className,"")) %in% modType(x))
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+  modName <- Modstrings::fullName(Biostrings:::XString(className,""))[f]
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+  modName
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+}
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+
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 # gets the first non virtual class which x extends from
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 .get_first_class_extends <- function(x){
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   e <- extends(class(x))
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@@ -14,11 +14,11 @@
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 \alias{plotCompareByCoord,ModifierSet,GRangesList-method}
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 \title{Comparison of Samples}
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 \usage{
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-compare(x, name, from = 1L, to = 30L, ...)
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+compare(x, name, pos = 1L, ...)
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 compareByCoord(x, coord, ...)
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-plotCompare(x, name, from = 1L, to = 30L, normalize, ...)
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+plotCompare(x, name, pos = 1L, normalize, ...)
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 plotCompareByCoord(x, coord, normalize, ...)
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@@ -29,8 +29,7 @@ plotCompareByCoord(x, coord, normalize, ...)
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 \S4method{compareByCoord}{ModifierSet,GRangesList}(x, coord, normalize,
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   ...)
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-\S4method{plotCompare}{ModifierSet}(x, name, from = 1L, to = 30L,
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-  normalize, ...)
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+\S4method{plotCompare}{ModifierSet}(x, name, pos = 1L, normalize, ...)
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 \S4method{plotCompareByCoord}{ModifierSet,GRanges}(x, coord, normalize,
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   ...)
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@@ -43,9 +42,7 @@ plotCompareByCoord(x, coord, normalize, ...)
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 \item{name}{Only for \code{compare}: the transcript name}
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-\item{from}{Only for \code{compare}: start position}
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-
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-\item{to}{Only for \code{compare}: end position}
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+\item{pos}{Only for \code{compare}: pos for comparison}
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 \item{...}{optional parameters:
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 \itemize{
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@@ -5,7 +5,6 @@
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 \name{subsetByCoord}
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 \alias{subsetByCoord}
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 \alias{labelByCoord}
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-\alias{subset,Modifier-method}
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 \alias{subsetByCoord,Modifier,GRanges-method}
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 \alias{subsetByCoord,Modifier,GRangesList-method}
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 \alias{subset,ModifierSet-method}
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@@ -15,6 +14,7 @@
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 \alias{labelByCoord,Modifier,GRangesList-method}
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 \alias{labelByCoord,ModifierSet,GRanges-method}
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 \alias{labelByCoord,ModifierSet,GRangesList-method}
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+\alias{subsetByCoord,SplitDataFrameList,GRanges-method}
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 \alias{subset,SequenceData-method}
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 \alias{subsetByCoord,SequenceData,GRanges-method}
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 \alias{subsetByCoord,SequenceData,GRangesList-method}
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@@ -24,7 +24,6 @@
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 \alias{subset,SequenceDataList-method}
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 \alias{subsetByCoord,SequenceDataList,GRanges-method}
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 \alias{subsetByCoord,SequenceDataList,GRangesList-method}
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-\alias{labelByCoord,SplitDataFrameList,GRanges-method}
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 \alias{labelByCoord,SequenceData,GRanges-method}
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 \alias{labelByCoord,SequenceData,GRangesList-method}
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 \alias{labelByCoord,SequenceDataSet,GRanges-method}
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@@ -38,8 +37,6 @@ subsetByCoord(x, coord, ...)
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 labelByCoord(x, coord, ...)
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-\S4method{subset}{Modifier}(x, name, pos = 1L, ...)
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-
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 \S4method{subsetByCoord}{Modifier,GRanges}(x, coord, ...)
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 \S4method{subsetByCoord}{Modifier,GRangesList}(x, coord, ...)
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@@ -58,6 +55,8 @@ labelByCoord(x, coord, ...)
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 \S4method{labelByCoord}{ModifierSet,GRangesList}(x, coord, ...)
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+\S4method{subsetByCoord}{SplitDataFrameList,GRanges}(x, coord, ...)
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+
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 \S4method{subset}{SequenceData}(x, name, pos = 1L, ...)
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 \S4method{subsetByCoord}{SequenceData,GRanges}(x, coord, ...)
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@@ -76,8 +75,6 @@ labelByCoord(x, coord, ...)
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 \S4method{subsetByCoord}{SequenceDataList,GRangesList}(x, coord, ...)
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-\S4method{labelByCoord}{SplitDataFrameList,GRanges}(x, coord, ...)
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-
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 \S4method{labelByCoord}{SequenceData,GRanges}(x, coord, ...)
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 \S4method{labelByCoord}{SequenceData,GRangesList}(x, coord, ...)
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@@ -98,9 +95,8 @@ labelByCoord(x, coord, ...)
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 a \code{GRangesList} object. For both types the 'Parent' column is expected to
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 match the transcript name.}
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-\item{...}{optional parameters:
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+\item{...}{Optional parameters:
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 \itemize{
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-\item{\code{name}:} {Limit results to one specific transcript.}
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 \item{\code{type}:} {the modification type used for subsetting. By default 
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 this is derived from the \code{modType(x)}, but it can be overwritten using 
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 \code{type}. It must be a valid shortName for a modification according to
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@@ -117,16 +113,20 @@ value \code{!= 0L} are set. (default: \code{merge = TRUE}).}
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 positions labeled per transcript and not per chromosome?
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 (default: \code{perTranscript = FALSE}).}
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 }}
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+
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+\item{name}{Optional: Limit results to one specific transcript.}
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+
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+\item{pos}{Optional: Limit results to a specific position.}
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 }
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 \value{
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 If 'x' is a
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 \itemize{
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 \item{\code{\link[=SequenceData-class]{SequenceData}} or 
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-\code{\link[=Modifier-class]{Modifier}}} {a \code{SplitDataFrameList}
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+\code{\link[=Modifier-class]{Modifier}}:} {a \code{SplitDataFrameList}
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 with elments per transcript.}
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 \item{\code{\link[=SequenceDataSet-class]{SequenceDataSet}},
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 \code{\link[=SequenceDataList-class]{SequenceDataList}} or
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-\code{\link[=ModifierSet-class]{ModifierSet}}} {a \code{SimpleList} of
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+\code{\link[=ModifierSet-class]{ModifierSet}}:} {a \code{SimpleList} of
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 \code{SplitDataFrameList} with elments per transcript.}
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 }
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 }