Commit ed786dfb authored by Aurelien Brionne's avatar Aurelien Brionne
Browse files

intron1 adding

parent e0f5d3c7
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'
......
......@@ -16,6 +16,5 @@ AutoAppendNewline: Yes
StripTrailingWhitespace: Yes
BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
PackageRoxygenize: rd,collate,namespace
......@@ -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
......
......@@ -17,6 +17,7 @@ setClass("genome_features",
UTR5="list",
exon="list",
intron="list",
intron1="list",
cds="list",
UTR3="list",
downstream="list",
......
......@@ -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
......
......@@ -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).
......
......@@ -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
)
}
......
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