first commit

DESCRIPTION

+Package: GenomeFeatures
+Version: 0.99.0
+Title: Multiple genomic features annotations
+Authors@R: c(
+	person("Aurelien","Brionne", role=c("aut","cre"),
+	email="aurelien.brionne@inra.fr"))
+Depends: R (>= 3.1.0)
+Imports:
+    AnnotationDbi,
+    data.table,
+    GenomicFeatures,
+    GenomicRanges,
+    IRanges,
+    methods,
+    plotly,
+   UpSetR
+Suggests:
+   BiocStyle,
+   knitr,
+   rmarkdown,
+   githubinstall
+Description: The aim of this package is to provide a full genomic features annotation from genomic coordinates, without use an annotation priority.
+VignetteBuilder: knitr
+License: MIT
+LazyData: TRUE
+Author: Aurelien Brionne [aut, cre]
+Maintainer: Aurelien Brionne <aurelien.brionne@inra.fr>
+Repository: gitHub
+RoxygenNote: 6.0.1
+Collate: 
+    'GFF_att.R'
+    'overlapped_genome_features.R'
+    'Plot.R'
+    'Table.R'
+    'genome_features.R'
+    'build_genome_features.R'
+    'genome_features_overlaps.R'
+    'readPeakFile.R'

GenomeFeatures.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

LICENSE

+YEAR: 2018
+COPYRIGHT HOLDER: Institut National de la Recherche Agronomique (INRA)

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(GFF_att)
+export(Plot)
+export(Table)
+export(build_genome_features)
+export(genome_features_overlaps)
+export(readPeakFile)
+import(data.table)
+importFrom(AnnotationDbi,as.data.frame)
+importFrom(AnnotationDbi,keys)
+importFrom(AnnotationDbi,metadata)
+importFrom(AnnotationDbi,select)
+importFrom(BiocGenerics,as.data.frame)
+importFrom(GenomicFeatures,cdsBy)
+importFrom(GenomicFeatures,exonsBy)
+importFrom(GenomicFeatures,fiveUTRsByTranscript)
+importFrom(GenomicFeatures,intronsByTranscript)
+importFrom(GenomicFeatures,promoters)
+importFrom(GenomicFeatures,threeUTRsByTranscript)
+importFrom(GenomicFeatures,transcripts)
+importFrom(GenomicRanges,GRanges)
+importFrom(GenomicRanges,flank)
+importFrom(GenomicRanges,pintersect)
+importFrom(IRanges,IRanges)
+importFrom(IRanges,findOverlaps)
+importFrom(IRanges,width)
+importFrom(S4Vectors,queryHits)
+importFrom(S4Vectors,subjectHits)
+importFrom(UpSetR,upset)
+importFrom(data.table,data.table)
+importFrom(data.table,fread)
+importFrom(grDevices,png)
+importFrom(methods,new)
+importFrom(methods,setClass)
+importFrom(methods,setMethod)
+importFrom(methods,slot)
+importFrom(methods,slotNames)
+importFrom(plotly,layout)
+importFrom(plotly,plot_ly)

R/GFF_att.R

+#' @title Extract attributes from gff.
+#' @description  Extract attributes from gff file  \code{\link[data.table]{data.table}}.
+#' @importFrom data.table data.table
+#' @details This internal function is use by \code{\link{build_genome_features}} in order to extract attributes from gff
+#' and return a  \code{\link[data.table]{data.table}}.
+#' @return a \code{\link[data.table]{data.table}}.
+#' @keywords internal
+#' @export
+GFF_att<-function(...,att.list=c("GeneID","Name","gene")){
+
+  #################
+  # Data loading
+  Data<-data.table::data.table(...)
+
+  #################
+  # extract attributes in table
+  Dat=base::lapply(att.list,function(y){
+
+    #################
+    # substitute
+    if(y=="ID"){
+
+      #################
+      # particular case
+      tmp<-base::gsub("ID=","",Data$att)
+
+    }else{
+
+      #################
+      # remove annotation before
+      tmp<-base::gsub(base::paste(".*",y,"[:=]",sep=""),"",Data$att)
+    }
+
+    #################
+    # remove annotation after
+    base::gsub("[;,].+","",tmp)
+  })
+
+  #################
+  # create data.table
+  require(data.table)
+  Dat=base::do.call("data.table",Dat)
+
+  #################
+  # add header
+  names(Dat)<-base::gsub(":|=","",att.list)
+
+  #################
+  # results table
+  return(data.table::data.table(Data,Dat))
+}

R/Plot.R

+#' @title  Plot overlapped_genome_features graphs.
+#' @description Plot overlapped_genome_features graphs bar or line.
+#' @param object an \code{\link{overlapped_genome_features-class}} object.
+#' @param type a \code{\link[base]{character}} which coulde be "bar" or "line".
+#' @details This method is a simple accessor to the stored \code{\link[plotly]{plot_ly}} bar or line plots from the \code{\link{overlapped_genome_features-class}} object.
+#' @return a \code{\link[plotly]{plot_ly}} object.
+#' @include overlapped_genome_features.R
+#' @examples
+#' ###################
+#'  # display bar plot
+#' GenomeFeatures::Plot(features_overlaps,"bar")
+#'
+#' ###################
+#'  # display bar plot
+#' GenomeFeatures::Plot(features_overlaps,"line")
+#' @export
+setGeneric(name="Plot",def=function(object,type){standardGeneric("Plot")})
+
+setMethod("Plot",signature="overlapped_genome_features",definition=function(object,type) {
+
+  ###################
+  # display graphs
+  switch(type,
+    bar=object@distribution$bar_plot,
+    line=object@distribution$lines_plot
+  )
+})

R/Table.R

+#' @title  extract the annotation table.
+#' @description extract the annotation table from an \code{\link{overlapped_genome_features-class}} object.
+#' @param object an \code{\link{overlapped_genome_features-class}} object.
+#' @details This method is a simple accessor to the stored genomic coordinates annnotation \code{\link[data.table]{data.table}}
+#' from an \code{\link{overlapped_genome_features-class}} object.
+#' @return a \code{\link[data.table]{data.table}} object.
+#' @include overlapped_genome_features.R
+#' @examples
+#' ###################
+#  # extract the annotation table
+#' annot<-GenomeFeatures::Table(features_overlaps)
+#' @export
+setGeneric(name="Table",def=function(object){standardGeneric("Table")})
+
+setMethod("Table",signature="overlapped_genome_features",definition=function(object){
+
+  ###################
+  # display the table
+  object@annotation
+})

R/build_genome_features.R

+#' @title  build a convenient genomic features object.
+#' @description build a convenient \code{\link{genome_features-class}} object needed for find overlaps beetween
+#' selected features and genomic coordinates in a single step.
+#' @importFrom  AnnotationDbi select keys as.data.frame metadata
+#' @importFrom  GenomicFeatures promoters transcripts fiveUTRsByTranscript threeUTRsByTranscript exonsBy intronsByTranscript cdsBy
+#' @importFrom  GenomicRanges flank
+#' @importFrom  BiocGenerics as.data.frame
+#' @importFrom  methods new
+#' @import data.table
+#' @param txdb a txdb database built with \pkg{GenomicFeatures} (see example).
+#' @param features a \code{\link[base]{vector}} of features \code{\link[base]{character}} with by
+#' default all the availables features ("promoter", "UTR5", "UTR3", "exon", "intron", "cds", and "downstream").
+#' @param parameters a \code{\link[base]{list}} of parameters to use in order to define promoter and
+#' downstream ranges distance to TSS (Transcript Start Site) or TES (Transcript End Site).
+#' \itemize{
+#'  \item{promoter_ranges: a \code{\link[base]{list}} with upstream and dowstream  elements distance (in base) to TSS}.
+#'  \item{downstream_range: the dowstream distance (in base) to the TES}.
+#' }
+#' @details This method build a convenient \code{\link{genomic_features-class}} object, in order to be used for finding overlaps beetween
+#' all selected features and genomic coordinates with the \code{\link{genome_features_overlaps}} method.
+#' @return a \code{\link{genome_features-class}} object.
+#' @include genome_features.R
+#' @examples
+#'
+#' ###################
+#  # import the chicken genome GFF from NCBI ftp (galGal5 in this case)
+#' utils::download.file("ftp://ftp.ncbi.nlm.nih.gov/genomes/Gallus_gallus/GFF/ref_Gallus_gallus-5.0_top_level.gff3.gz",
+#' quiet=T,destfile = "galGal5_gff.gz")
+#'
+#' ##################
+#' #  uncompress the file
+#' R.utils::gunzip("galGal5_gff.gz")
+#'
+#' ###################
+#' # build the database
+#' toplevel=GenomicFeatures::makeTxDbFromGFF(
+#'  file="galGal5_gff",
+#'  format="gff",
+#'  organism="Gallus gallus",
+#'  taxonomyId=9031,
+#'  dbxrefTag="ID"
+#' )
+#'
+#' ###################
+#' # build genome_features object from txdb
+#' features<-GenomeFeatures::build_genome_features(
+#'  toplevel,
+#'  features=base::c("promoter","UTR5","UTR3","exon","intron","cds","downstream"),
+#'  parameters = base::list(
+#'    promoter_ranges=base::list(
+#'      upstream=3000,
+#'      downstream=500
+#'    ),
+#'    downstream_range=1000
+#'  )
+#' )
+#' @export
+setGeneric(name="build_genome_features",def=function(txdb,features=base::c("promoter","UTR5","UTR3","exon","intron","cds","downstream"),
+parameters=base::list(promoter_ranges=base::list(upstream=3000,downstream=500),downstream_range=1000)){standardGeneric("build_genome_features")})
+
+setMethod("build_genome_features",definition=function(txdb,features=base::c("promoter","UTR5","UTR3","exon","intron","cds","downstream"),
+parameters=base::list(promoter_ranges=base::list(upstream=3000,downstream=500),downstream_range=1000)) {
+
+  ###################
+  # check txdb
+  ###################
+  if(base::class(txdb)!="TxDb") base::stop("txdb must be a TxDb class object")
+
+  ###################
+  # txdb ids crossref
+  ###################
+
+  ###################
+  # build ids cross reference
+  crossref<-data.table::data.table(
+    AnnotationDbi::select(txdb,columns=c("TXID","TXNAME"),
+    keytype="GENEID",keys=AnnotationDbi::keys(txdb))
+  )
+
+  ###################
+  # convert TXID to character
+  crossref[,TXID:=base::as.character(TXID)]
+
+  ###################
+  # promoters
+  ###################
+
+  promoters=NULL;promoters_DT=NULL
+
+  if("promoter"%in%features){
+
+    ###################
+    # get promoters
+    promoters <- GenomicFeatures::promoters(
+      txdb,
+      upstream=parameters$promoter_ranges$upstream,
+      downstream=parameters$promoter_ranges$upstream
+    )
+
+    ###################
+    # convert to table
+    promoters_DT<-data.table::data.table(AnnotationDbi::as.data.frame(promoters))[,.(tx_id,tx_name)]
+
+    ###################
+    # convert to character
+    promoters_DT[,tx_id:=base::as.character(tx_id)]
+
+    ###################
+    # merge with crossref
+    promoters_DT<-merge(promoters_DT,crossref,by.x="tx_id",by.y="TXID",sort=F,all.x=T)
+
+    ###################
+    # rename
+    base::names(promoters_DT)[1:2]<-base::c("group","feature")
+
+    ###################
+    # format feature
+    promoters_DT[,  tx_name:=feature]
+
+    ###################
+    # format feature
+    promoters_DT[,`:=`(
+      feature=base::paste(GENEID,feature,"promoter",sep=":"),
+      GENEID=NULL,
+      TXNAME=NULL
+    )]
+  }
+
+  ###################
+  # downstream
+  ###################
+
+  downstream=NULL;downstream_DT=NULL
+
+  if("downstream"%in%features){
+
+    ###################
+    # get downstream
+    downstream<- GenomicFeatures::transcripts(txdb)
+    downstream<-GenomicRanges::flank(downstream,parameters$downstream_range,start=F)
+
+    ###################
+    # convert to table
+    downstream_DT<-data.table::data.table(AnnotationDbi::as.data.frame(downstream))[,.(tx_id,tx_name)]
+
+    ###################
+    # convert to character
+    downstream_DT[,tx_id:=base::as.character(tx_id)]
+
+    ###################
+    # merge with crossref
+    downstream_DT<-merge(downstream_DT,crossref,by.x="tx_id",by.y="TXID",sort=F,all.x=T)
+
+    ###################
+    # rename
+    base::names(downstream_DT)[1:2]<-base::c("group","feature")
+
+    ###################
+    # format feature
+    downstream_DT[,tx_name:=feature]
+
+    ###################
+    # format feature
+    downstream_DT[,`:=`(
+      feature=base::paste(GENEID,feature,"downstream",sep=":"),
+      GENEID=NULL,
+      TXNAME=NULL
+    )]
+  }
+
+  ###################
+  # 5' UTR
+  ###################
+
+  UTR5=NULL;UTR5_DT=NULL
+
+  if("UTR5"%in%features){
+
+    ###################
+    # get 5' UTR in GRangesList
+    UTR5<-GenomicFeatures::fiveUTRsByTranscript(txdb,use.names=F)
+
+    ###################
+    # convert to table
+    UTR5_DT<-data.table::data.table(BiocGenerics::as.data.frame(UTR5))[,.(group_name,exon_rank)]
+
+    ###################
+    # convert to GRanges
+    UTR5<-base::unlist(UTR5)
+
+    ###################
+    # merge with crossref
+    UTR5_DT<-merge(UTR5_DT,crossref,by.x="group_name",by.y="TXID",sort=F,all.x=T)
+
+    ###################
+    # format feature
+    UTR5_DT[,`:=`(
+      feature=base::paste(GENEID,":",TXNAME,":5'UTR(exon",exon_rank,")",sep=""),
+      exon_rank=NULL,
+      GENEID=NULL,
+      tx_name=TXNAME,
+      TXNAME=NULL,
+      group_name=NULL
+    )]
+  }
+
+  ###################
+  # 3' UTR
+  ###################
+
+  UTR3=NULL;UTR3_DT=NULL
+
+  if("UTR3"%in%features){
+
+    ###################
+    # get 3' UTR
+    UTR3<-GenomicFeatures::threeUTRsByTranscript(txdb,use.names=F)
+
+    ###################
+    # convert to table
+    UTR3_DT<-data.table::data.table(AnnotationDbi::as.data.frame(UTR3))[,.(group_name,exon_rank)]
+
+    ###################
+    # convert to GRanges
+    UTR3<-base::unlist(UTR3)
+
+    ###################
+    # merge with crossref
+    UTR3_DT<-merge(UTR3_DT,crossref,by.x="group_name",by.y="TXID",sort=F,all.x=T)
+
+    ###################
+    # format feature
+    UTR3_DT[,`:=`(
+      feature=base::paste(GENEID,":",TXNAME,":3'UTR(exon",exon_rank,")",sep=""),
+      exon_rank=NULL,
+      GENEID=NULL,
+      tx_name=TXNAME,
+      TXNAME=NULL,
+      group_name=NULL
+    )]
+  }
+
+  ###################
+  # Exons
+  ###################
+
+  exons=NULL;exons_DT=NULL
+
+  if("exon"%in%features){
+
+    ###################
+    # get exons
+    exons<-GenomicFeatures::exonsBy(txdb,use.names=F)
+
+    ###################
+    # convert to table
+    exons_DT<-data.table::data.table(AnnotationDbi::as.data.frame(exons))[,.(group_name,exon_rank)]
+
+    ###################
+    # convert to GRanges
+    exons<-base::unlist(exons)
+
+    ###################
+    # count exons by transcripts
+    exons_nb<-exons_DT[!base::is.na(group_name),.N,by=group_name]
+
+    ###################
+    # merge count to exons_DT
+    exons_DT<-merge(exons_DT,exons_nb,by="group_name",all.x=T,sort=F)
+
+    ###################
+    # merge with crossref
+    exons_DT<-merge(exons_DT,crossref,by.x="group_name",by.y="TXID",sort=F,all.x=T)
+
+    ###################
+    # format feature
+    exons_DT[,`:=`(
+      feature=base::paste(GENEID,":",TXNAME,":exon",exon_rank,"/",N,sep=""),
+      exon_rank=NULL,
+      GENEID=NULL,
+      tx_name=TXNAME,
+      TXNAME=NULL,
+      N=NULL,
+      group_name=NULL
+    )]
+  }
+
+  ###################
+  # Introns
+  ###################
+
+  introns=NULL;introns_DT=NULL
+
+  if("intron"%in%features){
+
+    ###################
+    # get introns
+    introns<-GenomicFeatures::intronsByTranscript(txdb,use.names=F)
+
+    ###################
+    # convert to table
+    introns_DT<-data.table::data.table(AnnotationDbi::as.data.frame(introns))[,.(group_name,strand)]
+
+    ###################
+    # convert to GRanges
+    introns<-base::unlist(introns)
+
+    ###################
+    # count introns by transcripts
+    introns_nb<-introns_DT[!base::is.na(group_name),.N,by=group_name]
+
+    ###################
+    # merge count to introns_DT
+    introns_DT<-merge(introns_DT,introns_nb,by="group_name",all.x=T,sort=F)
+
+    ###################
+    # add intron_rank
+    introns_DT[,intron_rank:=1:base::length(N),by=group_name]
+
+    ###################
+    # reverse intron_rank for reverse strand
+    introns_DT[strand=="-",intron_rank:=base::rev(intron_rank),by=group_name]
+
+    ###################
+    # merge with crossref
+    introns_DT<-merge(introns_DT,crossref,by.x="group_name",by.y="TXID",sort=F,all.x=T)
+
+    ###################
+    # format feature
+    introns_DT[,`:=`(
+      feature=base::paste(GENEID,":",TXNAME,":intron",intron_rank,"/",N,sep=""),
+      intron_rank=NULL,
+      strand=NULL,
+      GENEID=NULL,
+      tx_name=TXNAME,
+      TXNAME=NULL,
+      N=NULL,
+      group_name=NULL
+    )]
+  }
+
+  ###################
+  # CDS
+  ###################
+
+  cds=NULL;cds_DT=NULL
+
+  if("cds"%in%features){
+
+    ###################
+    # get exons
+    cds<-GenomicFeatures::cdsBy(txdb,use.names=F)
+
+    ###################
+    # convert to table
+    cds_DT<-data.table::data.table(AnnotationDbi::as.data.frame(cds))[,.(group_name,exon_rank)]
+
+    ###################
+    # convert to GRanges
+    cds<-base::unlist(cds)
+
+    ###################
+    # count exons by transcripts
+    cds_nb<-cds_DT[!base::is.na(group_name),.N,by=group_name]
+
+    ###################
+    # merge count to exons_DT
+    cds_DT<-merge(cds_DT,cds_nb,by="group_name",all.x=T,sort=F)
+
+    ###################
+    # merge with crossref
+    cds_DT<-merge(cds_DT,crossref,by.x="group_name",by.y="TXID",sort=F,all.x=T)
+
+    ###################
+    # format feature
+    cds_DT[,`:=`(
+      feature=base::paste(GENEID,":",TXNAME,":exon",exon_rank,"/",N,sep=""),
+      exon_rank=NULL,
+      GENEID=NULL,
+      tx_name=TXNAME,
+      TXNAME=NULL,
+      N=NULL,
+      group_name=NULL
+    )]
+  }
+
+  ###################
+  # load annotation supplement
+  ###################
+
+  ###################
+  # read the gff
+  file=AnnotationDbi::metadata(txdb)$value[3]
+
+  ###################
+  # download
+  if(base::length(grep("ftp.+\\.gz$",file))>0){
+
+    ###################
+    # import the GFF
+    utils::download.file(file,quiet=T,destfile = "gff.gz")
+
+    ##################
+    #  uncompress
+    R.utils::gunzip("gff.gz")
+
+    ##################
+    # file to download
+    file="gff"
+  }
+
+  ###################
+  # read the gff
+  gff<-data.table::fread(file,fill=T,drop=base::c(2,6,8),verbose=F,showProgress=F,col.names=