intron1 adding

DESCRIPTION

 Package: GenomeFeatures
-Version: 1.0
+Version: 1.1
 Title: Multiple genomic features annotations
 Author: Aurelien Brionne [aut, cre]
 Maintainer: Aurelien Brionne <aurelien.brionne@inrae.fr>
@@ -29,11 +29,7 @@ VignetteBuilder: knitr
 License: GPL-3
 URL: https://forgemia.inra.fr/aurelien.brionne/GenomeFeatures
 BugReports: https://forgemia.inra.fr/aurelien.brionne/GenomeFeatures/issues
-<<<<<<< HEAD
 RoxygenNote: 7.1.1
-=======
-RoxygenNote: 7.1.0
->>>>>>> a1bed8b25cbc1b31ad4c962fe03a6ea43d5110f6
 Collate: 
     'GFF_att.R'
     'overlapped_genome_features.R'

GenomeFeatures.Rproj

@@ -16,6 +16,5 @@ AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 
 BuildType: Package
-PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageRoxygenize: rd,collate,namespace

R/build_genome_features.R

@@ -9,7 +9,7 @@
 #' @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").
+#' default all the availables features ("promoter", "UTR5", "UTR3", "exon", "intron","intron1", "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{
@@ -58,7 +58,7 @@
 setGeneric(
     name="build_genome_features",
     def=function(
-        txdb,features=c("promoter","UTR5","UTR3","exon","intron","cds","downstream"),
+        txdb,features=c("promoter","UTR5","UTR3","exon","intron","intron1","cds","downstream"),
         parameters=list(promoter_ranges=list(upstream=3000,downstream=500),downstream_range=1000)){
             standardGeneric("build_genome_features")
     }
@@ -369,8 +369,9 @@ setMethod(
         ## Introns
 
         introns=NULL;introns_DT=NULL
+        intron1=NULL;intron1_DT=NULL
 
-        if("intron"%in%features){
+        if("intron"%in%features | "intron1"%in%features){
 
             # get introns
             introns<-intronsByTranscript(txdb,use.names=FALSE)
@@ -436,6 +437,19 @@ setMethod(
                     group_name=NULL
                 )
             ]
+
+            if("intron1"%in%features){
+
+                # locate intron 1
+                pos<-grepl("intron1/",introns_DT[,feature])
+
+                # substet intron1
+                intron1_DT<-introns_DT[pos]
+
+                # get intron1 GRan
+                intron1<-introns[pos]
+
+            }
         }
 
         ## CDS
@@ -585,6 +599,7 @@ setMethod(
             UTR3=list(GRanges=UTR3,DT=UTR3_DT),
             exon=list(GRanges=exons,DT=exons_DT),
             intron=list(GRanges=introns,DT=introns_DT),
+            intron1=list(GRanges=intron1,DT=intron1_DT),
             cds=list(GRanges=cds,DT=cds_DT),
             downstream=list(GRanges=downstream,DT=downstream_DT),
             gene_table=gene_table

R/genome_features.R

@@ -17,6 +17,7 @@ setClass("genome_features",
            UTR5="list",
            exon="list",
            intron="list",
+           intron1="list",
            cds="list",
            UTR3="list",
            downstream="list",

README.md

@@ -24,7 +24,7 @@ remotes::install_gitlab(
     devtools::build("GenomeFeatures")
 
     # install package (from R console)
-    install.packages("GenomeFeatures_1.0.tar.gz", repos = NULL, type = "source")
+    install.packages("GenomeFeatures_1.1.tar.gz", repos = NULL, type = "source")
 ```
 
 ## Quick overview

man/build_genome_features-methods.Rd

@@ -7,14 +7,16 @@
 \usage{
 build_genome_features(
   txdb,
-  features = c("promoter", "UTR5", "UTR3", "exon", "intron", "cds", "downstream"),
+  features = c("promoter", "UTR5", "UTR3", "exon", "intron", "intron1", "cds",
+    "downstream"),
   parameters = list(promoter_ranges = list(upstream = 3000, downstream = 500),
     downstream_range = 1000)
 )
 
 \S4method{build_genome_features}{TxDb}(
   txdb,
-  features = c("promoter", "UTR5", "UTR3", "exon", "intron", "cds", "downstream"),
+  features = c("promoter", "UTR5", "UTR3", "exon", "intron", "intron1", "cds",
+    "downstream"),
   parameters = list(promoter_ranges = list(upstream = 3000, downstream = 500),
     downstream_range = 1000)
 )
@@ -23,7 +25,7 @@ build_genome_features(
 \item{txdb}{a txdb database built with \pkg{GenomicFeatures} (see example).}
 
 \item{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").}
+default all the availables features ("promoter", "UTR5", "UTR3", "exon", "intron","intron1", "cds", and "downstream").}
 
 \item{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).

man/genome_features_overlaps-methods.Rd

@@ -8,22 +8,14 @@
 genome_features_overlaps(
   peaks,
   features,
-<<<<<<< HEAD
-  figs_path = "./data/figs/",
-=======
   figs_path = ".",
->>>>>>> a1bed8b25cbc1b31ad4c962fe03a6ea43d5110f6
   ignore.strand = TRUE
 )
 
 \S4method{genome_features_overlaps}{CompressedGRangesList,genome_features}(
   peaks,
   features,
-<<<<<<< HEAD
-  figs_path = "./data/figs/",
-=======
   figs_path = ".",
->>>>>>> a1bed8b25cbc1b31ad4c962fe03a6ea43d5110f6
   ignore.strand = TRUE
 )
 }