@@ -791,11 +791,9 @@ setReplaceMethod(f = "settings",

   # search for modifications

   if(settings(ans,"find.mod")){

     if(seqtype(ans) == seqtype(RNAString())){

-      f <- which(Modstrings::shortName(Modstrings::ModRNAString()) %in% modType(ans))

-      modName <- Modstrings::fullName(Modstrings::ModRNAString())[f]

+      modName <- .get_modification_full_name(ans,seqtype(ans))

     } else if(seqtype(ans) == seqtype(DNAString())){

-      f <- which(Modstrings::shortName(Modstrings::ModDNAString()) %in% modType(ans))

-      modName <- Modstrings::fullName(Modstrings::ModDNAString())[f]

+      modName <- .get_modification_full_name(ans,seqtype(ans))

     } else {

       stop("")

     }

@@ -31,9 +31,10 @@ NULL

 #' @param coord coordinates of position to subset to. Either a \code{GRanges} or

 #' a \code{GRangesList} object. For both types the 'Parent' column is expected to

 #' match the transcript name.

-#' @param ... optional parameters:

+#' @param name Optional: Limit results to one specific transcript.

+#' @param pos Optional: Limit results to a specific position.

+#' @param ... Optional parameters:

 #' \itemize{

-#' \item{\code{name}:} {Limit results to one specific transcript.}

 #' \item{\code{type}:} {the modification type used for subsetting. By default 

 #' this is derived from the \code{modType(x)}, but it can be overwritten using 

 #' \code{type}. It must be a valid shortName for a modification according to

@@ -55,11 +56,11 @@ NULL

 #' If 'x' is a

 #' \itemize{

 #' \item{\code{\link[=SequenceData-class]{SequenceData}} or 

-#' \code{\link[=Modifier-class]{Modifier}}} {a \code{SplitDataFrameList}

+#' \code{\link[=Modifier-class]{Modifier}}:} {a \code{SplitDataFrameList}

 #' with elments per transcript.}

 #' \item{\code{\link[=SequenceDataSet-class]{SequenceDataSet}},

 #' \code{\link[=SequenceDataList-class]{SequenceDataList}} or

-#' \code{\link[=ModifierSet-class]{ModifierSet}}} {a \code{SimpleList} of

+#' \code{\link[=ModifierSet-class]{ModifierSet}}:} {a \code{SimpleList} of

 #' \code{SplitDataFrameList} with elments per transcript.}

 #' }

 #' 

@@ -110,8 +111,7 @@ NULL

   }

 }

-#' @rdname subsetByCoord

-#' @export

+#' @keywords internal

 setMethod("subset",

           signature = c(x = "Modifier"),

           function(x, name, pos = 1L, ...){

@@ -283,6 +283,8 @@ NULL

   coord

 }

+#' @rdname subsetByCoord

+#' @export

 setMethod("subsetByCoord",

           signature = c(x = "SplitDataFrameList", coord = "GRanges"),

           function(x, coord, ...){

@@ -448,8 +450,7 @@ setMethod("subsetByCoord",

   .keep_one_labels_column(ans)

 }

-#' @rdname subsetByCoord

-#' @export

+#' @keywords internal

 setMethod("labelByCoord",

           signature = c(x = "SplitDataFrameList", coord = "GRanges"),

           function(x, coord, ...){

@@ -1,6 +1,14 @@

 #' @include RNAmodR.R

 NULL

+.get_modification_full_name <- function(x, type = c("RNA","DNA")){

+  type <- match.arg(type)

+  className <- paste0("Mod",type)

+  f <- which(Modstrings::shortName(Biostrings:::XString(className,"")) %in% modType(x))

+  modName <- Modstrings::fullName(Biostrings:::XString(className,""))[f]

+  modName

+}

+

 # gets the first non virtual class which x extends from

 .get_first_class_extends <- function(x){

   e <- extends(class(x))

@@ -14,11 +14,11 @@

 \alias{plotCompareByCoord,ModifierSet,GRangesList-method}

 \title{Comparison of Samples}

 \usage{

-compare(x, name, from = 1L, to = 30L, ...)

+compare(x, name, pos = 1L, ...)

 compareByCoord(x, coord, ...)

-plotCompare(x, name, from = 1L, to = 30L, normalize, ...)

+plotCompare(x, name, pos = 1L, normalize, ...)

 plotCompareByCoord(x, coord, normalize, ...)

@@ -29,8 +29,7 @@ plotCompareByCoord(x, coord, normalize, ...)

 \S4method{compareByCoord}{ModifierSet,GRangesList}(x, coord, normalize,

   ...)

-\S4method{plotCompare}{ModifierSet}(x, name, from = 1L, to = 30L,

-  normalize, ...)

+\S4method{plotCompare}{ModifierSet}(x, name, pos = 1L, normalize, ...)

 \S4method{plotCompareByCoord}{ModifierSet,GRanges}(x, coord, normalize,

   ...)

@@ -43,9 +42,7 @@ plotCompareByCoord(x, coord, normalize, ...)

 \item{name}{Only for \code{compare}: the transcript name}

-\item{from}{Only for \code{compare}: start position}

-

-\item{to}{Only for \code{compare}: end position}

+\item{pos}{Only for \code{compare}: pos for comparison}

 \item{...}{optional parameters:

 \itemize{

@@ -5,7 +5,6 @@

 \name{subsetByCoord}

 \alias{subsetByCoord}

 \alias{labelByCoord}

-\alias{subset,Modifier-method}

 \alias{subsetByCoord,Modifier,GRanges-method}

 \alias{subsetByCoord,Modifier,GRangesList-method}

 \alias{subset,ModifierSet-method}

@@ -15,6 +14,7 @@

 \alias{labelByCoord,Modifier,GRangesList-method}

 \alias{labelByCoord,ModifierSet,GRanges-method}

 \alias{labelByCoord,ModifierSet,GRangesList-method}

+\alias{subsetByCoord,SplitDataFrameList,GRanges-method}

 \alias{subset,SequenceData-method}

 \alias{subsetByCoord,SequenceData,GRanges-method}

 \alias{subsetByCoord,SequenceData,GRangesList-method}

@@ -24,7 +24,6 @@

 \alias{subset,SequenceDataList-method}

 \alias{subsetByCoord,SequenceDataList,GRanges-method}

 \alias{subsetByCoord,SequenceDataList,GRangesList-method}

-\alias{labelByCoord,SplitDataFrameList,GRanges-method}

 \alias{labelByCoord,SequenceData,GRanges-method}

 \alias{labelByCoord,SequenceData,GRangesList-method}

 \alias{labelByCoord,SequenceDataSet,GRanges-method}

@@ -38,8 +37,6 @@ subsetByCoord(x, coord, ...)

 labelByCoord(x, coord, ...)

-\S4method{subset}{Modifier}(x, name, pos = 1L, ...)

-

 \S4method{subsetByCoord}{Modifier,GRanges}(x, coord, ...)

 \S4method{subsetByCoord}{Modifier,GRangesList}(x, coord, ...)

@@ -58,6 +55,8 @@ labelByCoord(x, coord, ...)

 \S4method{labelByCoord}{ModifierSet,GRangesList}(x, coord, ...)

+\S4method{subsetByCoord}{SplitDataFrameList,GRanges}(x, coord, ...)

+

 \S4method{subset}{SequenceData}(x, name, pos = 1L, ...)

 \S4method{subsetByCoord}{SequenceData,GRanges}(x, coord, ...)

@@ -76,8 +75,6 @@ labelByCoord(x, coord, ...)

 \S4method{subsetByCoord}{SequenceDataList,GRangesList}(x, coord, ...)

-\S4method{labelByCoord}{SplitDataFrameList,GRanges}(x, coord, ...)

-

 \S4method{labelByCoord}{SequenceData,GRanges}(x, coord, ...)

 \S4method{labelByCoord}{SequenceData,GRangesList}(x, coord, ...)

@@ -98,9 +95,8 @@ labelByCoord(x, coord, ...)

 a \code{GRangesList} object. For both types the 'Parent' column is expected to

 match the transcript name.}

-\item{...}{optional parameters:

+\item{...}{Optional parameters:

 \itemize{

-\item{\code{name}:} {Limit results to one specific transcript.}

 \item{\code{type}:} {the modification type used for subsetting. By default 

 this is derived from the \code{modType(x)}, but it can be overwritten using 

 \code{type}. It must be a valid shortName for a modification according to

@@ -117,16 +113,20 @@ value \code{!= 0L} are set. (default: \code{merge = TRUE}).}

 positions labeled per transcript and not per chromosome?

 (default: \code{perTranscript = FALSE}).}

 }}

+

+\item{name}{Optional: Limit results to one specific transcript.}

+

+\item{pos}{Optional: Limit results to a specific position.}

 }

 \value{

 If 'x' is a

 \itemize{

 \item{\code{\link[=SequenceData-class]{SequenceData}} or 

-\code{\link[=Modifier-class]{Modifier}}} {a \code{SplitDataFrameList}

+\code{\link[=Modifier-class]{Modifier}}:} {a \code{SplitDataFrameList}

 with elments per transcript.}

 \item{\code{\link[=SequenceDataSet-class]{SequenceDataSet}},

 \code{\link[=SequenceDataList-class]{SequenceDataList}} or

-\code{\link[=ModifierSet-class]{ModifierSet}}} {a \code{SimpleList} of

+\code{\link[=ModifierSet-class]{ModifierSet}}:} {a \code{SimpleList} of

 \code{SplitDataFrameList} with elments per transcript.}

 }

 }