@@ -1,7 +1,7 @@

 Package: RNAmodR

 Type: Package

 Title: Detection of post-transcriptional modifications in high throughput sequencing data

-Version: 0.99.29

+Version: 0.99.30

 Date: 2019-06-11

 Authors@R: c(person("Felix G.M.", 

                     "Ernst", 

@@ -17,7 +17,7 @@ Description: RNAmodR provides classes and workflows for loading/aggregation data

     modifications through analysis of specific patterns. In addition, utilities

     are provided to validate and visualize the results. The RNAmodR package

     provides a core functionality from which specific analysis strategies can

-    be easily implemented as seperate package.

+    be easily implemented as a seperate package.

 biocViews: 

     Software, Infrastructure, WorkflowStep, Visualization, Sequencing

 License: Artistic-2.0

@@ -37,12 +37,12 @@ Imports:

     grid,

     matrixStats,

     assertive,

-    XVector,

     BiocGenerics,

+    XVector,

+    Biostrings,

     BiocParallel,

     GenomicFeatures,

     GenomicAlignments,

-    Biostrings,

     GenomeInfoDb,

     rtracklayer,

     Rsamtools,

@@ -55,7 +55,6 @@ Imports:

     reshape2,

     stringi,

     stringr,

-    dplyr,

     ROCR

 Suggests:

     BiocStyle,

@@ -120,6 +120,7 @@ exportMethods(settings)

 exportMethods(subsetByCoord)

 exportMethods(validAggregate)

 exportMethods(validModification)

+import(BiocGenerics)

 import(GenomicRanges)

 import(Gviz)

 import(S4Vectors)

@@ -137,9 +138,6 @@ importClassesFrom(IRanges,SplitDataFrameList)

 importClassesFrom(Rsamtools,BamFileList)

 importClassesFrom(Rsamtools,PileupFiles)

 importFrom(BSgenome,seqnames)

-importFrom(BiocGenerics,conditions)

-importFrom(BiocGenerics,path)

-importFrom(BiocGenerics,which)

 importFrom(BiocParallel,SerialParam)

 importFrom(BiocParallel,bplapply)

 importFrom(BiocParallel,bpmapply)

@@ -184,7 +182,6 @@ importFrom(Rsamtools,scanFa)

 importFrom(S4Vectors,splitAsList)

 importFrom(biovizBase,getBioColor)

 importFrom(colorRamps,matlab.like)

-importFrom(dplyr,mutate_)

 importFrom(ggplot2,geom_raster)

 importFrom(ggplot2,ggplot)

 importFrom(grDevices,col2rgb)

@@ -197,7 +194,6 @@ importFrom(matrixStats,rowSds)

 importFrom(reshape2,dcast)

 importFrom(reshape2,melt)

 importFrom(rtracklayer,GFF3File)

-importFrom(stats,D)

 importFrom(stats,setNames)

 importFrom(stringi,stri_rand_strings)

 importFrom(stringr,str_detect)

@@ -337,7 +337,6 @@ S4Vectors::setValidity2(Class = "Modifier", .valid_Modifier)

 }

 #' @rdname Modifier-functions

-#' @importFrom BiocGenerics path

 setMethod(

   f = "show",

   signature = signature(object = "Modifier"),

@@ -231,7 +231,6 @@ NULL

 }

 #' @importFrom graphics par abline title legend plot.new

-#' @importFrom colorRamps matlab.like

 #' @importFrom ROCR prediction performance

 .plot_ROCR <- function(data, prediction.args, performance.args, plot.args,

                        score){

@@ -1,44 +1,6 @@

 #' @include RNAmodR.R

 NULL

-# error propagation ------------------------------------------------------------

-

-################################################################################

-# modified from Lee Pang, 2015,

-# (https://oddhypothesis.blogspot.com/2015/01/easy-error-propagation-in-r.html)

-# (https://www.r-bloggers.com/easy-error-propagation-in-r/)

-################################################################################

-

-#' @importFrom dplyr mutate_

-#' @importFrom stats D

-.mutate_with_error <- function(.data, f){

-  exprs = list(

-    # expression to compute new variable values

-    deparse(f[[3]]),

-    # expression to compute new variable errors

-    sprintf('sqrt(%s)',

-            paste(vapply(all.vars(f[[3]]),

-                         function(v) {

-                           dfdp = deparse(stats::D(f[[3]], 

-                                                   v))

-                           sprintf('(d%s*(%s))^2', 

-                                   v,

-                                   dfdp)

-                         },

-                         character(1)),

-                  collapse = '+'))

-  )

-  names(exprs) = c(

-    deparse(f[[2]]),

-    sprintf('d%s', deparse(f[[2]]))

-  )

-  if( nrow(.data) > 0 ){

-    # the standard evaluation alternative of mutate()

-    .data <- dplyr::mutate_(.data, .dots = exprs)

-  }

-  return(.data)

-}

-

 # construct GRanges object from found modifications ----------------------------

 #' @rdname RNAmodR-development

@@ -166,7 +166,6 @@ setMethod(f = "relistToClass",

 }

 #' @importFrom Rsamtools BamFileList 

-#' @importFrom BiocGenerics path

 .contains_only_bamfiles <- function(x){

   x <- unname(x)

   classNames <- vapply(x, function(z){class(z)[[1]]},character(1))

@@ -326,6 +326,7 @@ setMethod("compareByCoord",

 }

 #' @importFrom ggplot2 ggplot geom_raster

+#' @importFrom colorRamps matlab.like

 #' @importFrom reshape2 melt

 .plot_compare_ModifierSet_by_GRanges <- function(x, coord, normalize,  ...){

   args <- .norm_compare_plot_args(list(...))

@@ -65,10 +65,10 @@ NULL

 #' @import methods

 #' @import assertive

-#' @import XVector

 #' @import S4Vectors

 #' @import GenomicRanges

-#' @importFrom BiocGenerics which conditions

+#' @import BiocGenerics

+#' @import XVector

 #' @importFrom Biostrings DNAString RNAString DNAStringSet RNAStringSet getSeq

 #' @importFrom Modstrings ModRNAString ModRNAStringSet combineIntoModstrings

 #' shortName fullName

@@ -825,6 +825,11 @@ setMethod(f = "seqinfo",

 setMethod(f = "sequences", 

           signature = signature(x = "SequenceData"),

           definition = function(x){relist(sequences(unlist(x)),x)})

+#' @rdname SequenceData-functions

+#' @export

+setMethod(f = "dataType",

+          signature = signature(x = "SequenceData"),

+          definition = function(x){dataType(unlist(x))})

 # dummy functions --------------------------------------------------------------

 # this needs to be implemented by each subclass

@@ -256,6 +256,11 @@ setMethod(

   f = "seqinfo", 

   signature = signature(x = "SequenceDataFrame"),

   definition = function(x){x@seqinfo})

+#' @rdname SequenceData-functions

+#' @export

+setMethod(f = "dataType",

+          signature = signature(x = "SequenceDataFrame"),

+          definition = function(x){gsub("SequenceDataFrame","",class(x))})

 # internals --------------------------------------------------------------------

@@ -3,8 +3,7 @@ NULL

 # Annotation -------------------------------------------------------------------

-#' @importFrom rtracklayer GFF3File 

-#' @importFrom BiocGenerics path

+#' @importFrom rtracklayer GFF3File

 .norm_gff <- function(x, className, .xname = assertive::get_name_in_parent(x)){

   if(!is(x,"GFF3File")){

     x <- try(rtracklayer::GFF3File(x), silent = TRUE)

@@ -22,7 +21,6 @@ NULL

 }

 #' @importFrom GenomicFeatures makeTxDbFromGFF

-#' @importFrom BiocGenerics path

 # Returns a TxDb or a GRangesList object

 .norm_annotation <- function(annotation, className, 

                   .annotationname = assertive::get_name_in_parent(annotation)){

@@ -63,7 +61,6 @@ NULL

 # Sequences --------------------------------------------------------------------

 #' @importFrom Rsamtools FaFile

-#' @importFrom BiocGenerics path

 # Either return a FaFile or BSgenome object

 .norm_sequences <- function(seq, className){

   if(!is(seq,"FaFile") && !is(seq,"BSgenome")){

@@ -92,7 +89,6 @@ NULL

 SAMPLE_TYPES <- c("treated","control")

 #' @importFrom Rsamtools BamFileList

-#' @importFrom BiocGenerics path

 .norm_bamfiles <- function(x, className, 

                            .xname = assertive::get_name_in_parent(x)){

   if(is.list(x)){

@@ -13,6 +13,7 @@

 \alias{conditions,SequenceDataFrame-method}

 \alias{bamfiles,SequenceDataFrame-method}

 \alias{seqinfo,SequenceDataFrame-method}

+\alias{dataType,SequenceDataFrame-method}

 \alias{show,SequenceData-method}

 \alias{getData,SequenceData,BamFileList,GRangesList,XStringSet,ScanBamParam-method}

 \alias{bamfiles,SequenceData-method}

@@ -21,6 +22,7 @@

 \alias{replicates,SequenceData-method}

 \alias{seqinfo,SequenceData-method}

 \alias{sequences,SequenceData-method}

+\alias{dataType,SequenceData-method}

 \alias{show,SequenceDataSet-method}

 \alias{seqinfo,SequenceDataSet-method}

 \alias{names,SequenceDataSet-method}

@@ -56,6 +58,8 @@ replicates(x)

 \S4method{seqinfo}{SequenceDataFrame}(x)

+\S4method{dataType}{SequenceDataFrame}(x)

+

 \S4method{show}{SequenceData}(object)

@@ -74,6 +78,8 @@ replicates(x)

 \S4method{sequences}{SequenceData}(x)

+\S4method{dataType}{SequenceData}(x)

+

 \S4method{show}{SequenceDataSet}(object)

 \S4method{seqinfo}{SequenceDataSet}(x)