bioconductor code style update

DESCRIPTION

@@ -3,8 +3,9 @@ Version: 1.0
 Title: Multiple genomic features annotations
 Author: Aurelien Brionne [aut, cre]
 Maintainer: Aurelien Brionne <aurelien.brionne@inra.fr>
-Depends: R (>= 3.5)
+Depends: R (>= 3.6)
 Imports:AnnotationDbi,
+        BiocGenerics,
         data.table,
         GenomicFeatures,
         GenomicRanges,
@@ -12,6 +13,7 @@ Imports:AnnotationDbi,
         methods,
         plotly,
         rtracklayer,
+        S4Vectors,
         UpSetR
 Suggests: htmltools,
           org.Mm.eg.db,

NAMESPACE

@@ -6,7 +6,6 @@ exportMethods(Plot)
 exportMethods(Table)
 exportMethods(build_genome_features)
 exportMethods(genome_features_overlaps)
-import(data.table)
 importFrom(AnnotationDbi,as.data.frame)
 importFrom(AnnotationDbi,keys)
 importFrom(AnnotationDbi,metadata)
@@ -28,17 +27,21 @@ importFrom(IRanges,width)
 importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,subjectHits)
 importFrom(UpSetR,upset)
+importFrom(data.table,":=")
+importFrom(data.table,.N)
+importFrom(data.table,.SD)
 importFrom(data.table,data.table)
+importFrom(data.table,dcast)
 importFrom(data.table,fread)
+importFrom(data.table,like)
+importFrom(data.table,melt)
+importFrom(data.table,rbindlist)
+importFrom(data.table,setorder)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,png)
-importFrom(methods,is)
-importFrom(methods,new)
-importFrom(methods,setClass)
 importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,slot)
-importFrom(methods,slotNames)
 importFrom(plotly,layout)
 importFrom(plotly,plot_ly)
 importFrom(rtracklayer,import)

R/Plot.R

@@ -7,11 +7,13 @@
 #' @return a \code{\link[plotly]{plot_ly}} object.
 #' @include overlapped_genome_features.R
 #' @examples
+#' \dontrun{
 #' # display bar plot
 #' Plot(features_overlaps,"bar")
 #'
 #' # display bar plot
 #' Plot(features_overlaps,"line")
+#' }
 #' @name Plot
 #' @rdname Plot-methods
 #' @exportMethod Plot

R/build_genome_features.R

@@ -6,7 +6,7 @@
 #' @importFrom  GenomicRanges flank
 #' @importFrom rtracklayer import
 #' @importFrom  BiocGenerics as.data.frame
-#' @importFrom data.table data.table := .N
+#' @importFrom data.table data.table := .N like
 #' @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").
@@ -28,7 +28,7 @@
 #'     destfile = "galGal5_gff.gz"
 #' )
 #'
-#' #  uncompress the file
+#' # uncompress the file
 #' R.gunzip("galGal5_gff.gz")
 #'
 #' # build the database

R/genome_features_overlaps.R

@@ -109,7 +109,7 @@ setMethod(
 
                     # subject_coordinates
                     feature_coordinates=data.table(
-                        as.data.frame(
+                        base::as.data.frame(
                             subject[subjectHits(hits)]
                         )
                     )

man/Plot-methods.Rd

@@ -25,11 +25,11 @@ Plot overlapped_genome_features graphs bar or line.
 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.
 }
 \examples{
-###################
- # display bar plot
-GenomeFeatures::Plot(features_overlaps,"bar")
+\dontrun{
+# display bar plot
+Plot(features_overlaps,"bar")
 
-###################
- # display bar plot
-GenomeFeatures::Plot(features_overlaps,"line")
+# display bar plot
+Plot(features_overlaps,"line")
+}
 }

man/Table-methods.Rd

@@ -24,6 +24,6 @@ This method is a simple accessor to the stored genomic coordinates annnotation \
 from an \code{\link{overlapped_genome_features-class}} object.
 }
 \examples{
-###################
-annot<-GenomeFeatures::Table(features_overlaps)
+# extract the annotation table
+annot<-Table(features_overlaps)
 }

man/build_genome_features-methods.Rd

@@ -6,15 +6,15 @@
 \alias{build_genome_features,TxDb-method}
 \title{build a convenient genomic features object.}
 \usage{
-build_genome_features(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))
+build_genome_features(txdb, features = c("promoter", "UTR5", "UTR3",
+  "exon", "intron", "cds", "downstream"),
+  parameters = list(promoter_ranges = list(upstream = 3000, downstream =
+  500), downstream_range = 1000))
 
-\S4method{build_genome_features}{TxDb}(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))
+\S4method{build_genome_features}{TxDb}(txdb, features = c("promoter",
+  "UTR5", "UTR3", "exon", "intron", "cds", "downstream"),
+  parameters = list(promoter_ranges = list(upstream = 3000, downstream =
+  500), downstream_range = 1000))
 }
 \arguments{
 \item{txdb}{a txdb database built with \pkg{GenomicFeatures} (see example).}
@@ -41,36 +41,34 @@ This method build a convenient \code{\link{genomic_features-class}} object, in o
 all selected features and genomic coordinates with the \code{\link{genome_features_overlaps}} method.
 }
 \examples{
+download.file(
+    "ftp://ftp.ncbi.nlm.nih.gov/genomes/Gallus_gallus/GFF/ref_Gallus_gallus-5.0_top_level.gff3.gz",
+    quiet=TRUE,
+    destfile = "galGal5_gff.gz"
+)
 
-###################
-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")
+# uncompress the file
+R.gunzip("galGal5_gff.gz")
 
-###################
 # build the database
-toplevel=GenomicFeatures::makeTxDbFromGFF(
- file="galGal5_gff",
- format="gff",
- organism="Gallus gallus",
- taxonomyId=9031,
- dbxrefTag="ID"
+toplevel=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
- )
+    toplevel,
+    features=c("promoter","UTR5","UTR3","exon","intron","cds","downstream"),
+    parameters = list(
+        promoter_ranges=list(
+            upstream=3000,
+            downstream=500
+        ),
+        downstream_range=1000
+    )
 )
 }

man/genome_features-class.Rd

@@ -6,7 +6,6 @@
 \title{genome_features class object definition.}
 \description{
 This class is invoked by \code{\link{build_genome_features}} method in order to store for each features
-a \code{\link[base]{list}} with \code{\link[GenomicRanges]{GRanges}} and \code{\link[data.table]{data.table}} elements.
 }
 \section{Slots}{
 

man/genome_features_overlaps-methods.Rd

@@ -33,11 +33,10 @@ This method build a convenient genomic features object, in order to be used for
 all needed features and peaks coordinates with \code{\link{genome_features_overlaps}}.
 }
 \examples{
-###################
 features_overlaps<-GenomeFeatures::genome_features_overlaps(
- peaks,
- features,
- figs_path="./data/output/",
- ignore.strand = TRUE
+    peaks,
+    features,
+    figs_path="./data/output/",
+    ignore.strand = TRUE
 )
 }

man/readPeakFile.Rd

@@ -20,12 +20,11 @@ and to convert it in \code{\link[GenomicRanges]{GRanges}} object.
 This function read peaks coordinates file (bed file) and store the results in a \code{\link[GenomicRanges]{GRanges}} object.
 }
 \examples{
-###################
 # read peak file (package sample from NCBI)
 peaks<-GenomeFeatures::readPeakFile(
- base::system.file(
-  "extdata/data/input/A.bed",
-  package="GenomeFeatures"
- )
+    system.file(
+        "extdata/data/input/A.bed",
+        package="GenomeFeatures"
+    )
 )
 }

vignettes/GenomeFeatures.Rmd

@@ -11,16 +11,14 @@ vignette: >
   %\VignetteIndexEntry{GenomeFeatures}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
-bibliography: "`r base::system.file('extdata/','bibliography.bib',package='GenomeFeatures')`"
-csl: "`r base::system.file('extdata/','bmc-genomics.csl',package='GenomeFeatures')`"
+bibliography: "`r system.file('extdata/','bibliography.bib',package='GenomeFeatures')`"
+csl: "`r system.file('extdata/','bmc-genomics.csl',package='GenomeFeatures')`"
 ---
 
 ```{r setup,include=FALSE}
-###################
 # load library
 library(GenomeFeatures)
 
-###################
 # knitr document options
 knitr::opts_chunk$set(eval=TRUE,echo=TRUE, message=FALSE,comment=NA,warning=FALSE)
 ```
@@ -38,24 +36,23 @@ In this vignette, we use only the chicken (galGal5) chromosome 1 (NC_006088.4) t
 
 ## Load the genomic coordinates targets
 
-At the first step we read peaks files (also known bed files with genomic coordinates chr, start, end, strand) in a `base::list`, and convert it in GRanges object with `GenomeFeatures::readPeakFile`.
+At the first step we read peaks files (also known bed files with genomic coordinates chr, start, end, strand) in a `list`, and convert it in GRanges object with `GenomeFeatures::readPeakFile`.
 
 ```{r peaks}
-###################
 # load peak files 
 peaks=GenomicRanges::GRangesList(
-  A=GenomeFeatures::readPeakFile(
-   base::system.file(
-     "extdata/data/input/A.bed",
-     package="GenomeFeatures"
-    )
-  ),
- B=GenomeFeatures::readPeakFile(
-   base::system.file(
-     "extdata/data/input/B.bed",
-     package="GenomeFeatures"
+    A=GenomeFeatures::readPeakFile(
+        system.file(
+            "extdata/data/input/A.bed",
+            package="GenomeFeatures"
+        )
+    ),
+     B=GenomeFeatures::readPeakFile(
+        system.file(
+            "extdata/data/input/B.bed",
+            package="GenomeFeatures"
+        )
     )
-  )
 )
 ```
 
@@ -64,56 +61,54 @@ peaks=GenomicRanges::GRangesList(
 For this vignette, we build the transcript database from the chicken gff with `GenomicFeatures::makeTxDbFromGFF` @GenomicFeatures.
 
 ```{r gff,eval=FALSE}
-###################
 # import the GFF (galGal5 chicken GFF 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")
-    
-##################
+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")
+gunzip("galGal5_gff.gz")
 ```
 
 <u>Important note:</u> In this vignette, we use only a part of the chicken (galGal5) chromosome 1 (NC_006088.4) gff to illustrate  `GenomeFeatures` results.
 
 ```{r TxDb_build}
-###################
 # build the database
 toplevel=GenomicFeatures::makeTxDbFromGFF(
-  file= base::system.file(
-     "/extdata/data/input/galGal5.gff",
-     package="GenomeFeatures"
+    file= system.file(
+        "/extdata/data/input/galGal5.gff",
+        package="GenomeFeatures"
     ),
-  format="gff",
-  organism="Gallus gallus",
-  taxonomyId=9031,
-  dbxrefTag="ID"
+    format="gff",
+    organism="Gallus gallus",
+    taxonomyId=9031,
+    dbxrefTag="ID"
 )
 ```
 
 Now, we build a convenient object with `GenomeFeatures::build_genome_features`, needed for find overlaps beetween all selected features and genomic coordinates targets into a single step (see below).
 
 ```{r features}
-###################
 # build genome features
-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
-  )
+features<-build_genome_features(
+    toplevel,
+    features=c("promoter","UTR5","UTR3","exon","intron","cds","downstream"),
+    parameters = list(
+        promoter_ranges=list(
+            upstream=3000,
+            downstream=500
+        ),
+        downstream_range=1000
+    )
 )
 ```
 
 We can display a short summary.
 
 ```{r features_display}
-###################
-# build genome features
+# show summary
 features
 ```
 
@@ -122,12 +117,11 @@ features
 Now we can find all overlaps beetween targets coordinates and the needed genomic features with `GenomeFeatures::genome_features_overlaps`.
 
 ```{r overlaps}
-###################
 # find overlapss
 features_overlaps<-GenomeFeatures::genome_features_overlaps(
   peaks,
   features,
-  figs_path=base::system.file(
+  figs_path=system.file(
     "/extdata/data/output/",
     package="GenomeFeatures"
   ),
@@ -185,10 +179,10 @@ We can also display the `UpSetR::upset` plot previously built by`GenomeFeatures:
 
 * A
 
-<img src="`r base::system.file("extdata/data/output/upset_A.png",package="GenomeFeatures")`" alt="Drawing" style="width: 800px;"/>
+<img src="`r system.file("extdata/data/output/upset_A.png",package="GenomeFeatures")`" alt="Drawing" style="width: 800px;"/>
 
 * B
 
-<img src="`r base::system.file("extdata/data/output/upset_B.png",package="GenomeFeatures")`" alt="Drawing" style="width: 800px;"/>
+<img src="`r system.file("extdata/data/output/upset_B.png",package="GenomeFeatures")`" alt="Drawing" style="width: 800px;"/>
 
 # References