Commit ddf5cc72 authored by Aurelien Brionne's avatar Aurelien Brionne
Browse files

update

parent c06a6116
...@@ -4,7 +4,7 @@ Title: Multiple genomic features annotations ...@@ -4,7 +4,7 @@ Title: Multiple genomic features annotations
Author: Aurelien Brionne [aut, cre] Author: Aurelien Brionne [aut, cre]
Maintainer: Aurelien Brionne <aurelien.brionne@inra.fr> Maintainer: Aurelien Brionne <aurelien.brionne@inra.fr>
Depends: R (>= 3.6) Depends: R (>= 3.6)
Imports:AnnotationDbi, Imports: AnnotationDbi,
BiocGenerics, BiocGenerics,
data.table, data.table,
GenomicFeatures, GenomicFeatures,
...@@ -29,7 +29,7 @@ VignetteBuilder: knitr ...@@ -29,7 +29,7 @@ VignetteBuilder: knitr
License: GPL-3 License: GPL-3
URL: https://forgemia.inra.fr/aurelien.brionne/GenomeFeatures URL: https://forgemia.inra.fr/aurelien.brionne/GenomeFeatures
BugReports: https://forgemia.inra.fr/aurelien.brionne/GenomeFeatures/issues BugReports: https://forgemia.inra.fr/aurelien.brionne/GenomeFeatures/issues
RoxygenNote: 6.1.1 RoxygenNote: 7.1.1
Collate: Collate:
'GFF_att.R' 'GFF_att.R'
'overlapped_genome_features.R' 'overlapped_genome_features.R'
......
...@@ -10,7 +10,7 @@ ...@@ -10,7 +10,7 @@
#' @importFrom data.table data.table rbindlist .SD .N := melt setorder dcast #' @importFrom data.table data.table rbindlist .SD .N := melt setorder dcast
#' @param peaks a \code{\link[base]{list}} of \code{\link[GenomicRanges]{GRanges}} objects elements provided by \code{\link{readPeakFile}}. #' @param peaks a \code{\link[base]{list}} of \code{\link[GenomicRanges]{GRanges}} objects elements provided by \code{\link{readPeakFile}}.
#' @param features a \code{\link{genome_features-class}} object. #' @param features a \code{\link{genome_features-class}} object.
#' @param figs_path the path where print the \code{\link[UpSetR]{upstet}} plots. ("./data/figs/", by default). #' @param figs_path the path where print the \code{\link[UpSetR]{upset}} plots. ("./data/figs/", by default).
#' @param ignore.strand ignore peak coordinate orientation (defaul to TRUE). #' @param ignore.strand ignore peak coordinate orientation (defaul to TRUE).
#' @details This method build a convenient genomic features object, in order to be used for finding overlaps beetween #' @details This method build a convenient genomic features object, in order to be used for finding overlaps beetween
#' all needed features and peaks coordinates with \code{\link{genome_features_overlaps}}. #' all needed features and peaks coordinates with \code{\link{genome_features_overlaps}}.
...@@ -371,10 +371,12 @@ setMethod( ...@@ -371,10 +371,12 @@ setMethod(
# create upset # create upset
png(paste(figs_path,"upset_",x,".png",sep="")) png(paste(figs_path,"upset_",x,".png",sep=""))
upset( print(
Data,sets=rev(names(Data)[-1]), upset(
sets.bar.color=rev(colors), Data,sets=rev(names(Data)[-1]),
keep.order = TRUE sets.bar.color=rev(colors),
keep.order = TRUE
)
) )
dev.off() dev.off()
}) })
......
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Plot.R % Please edit documentation in R/Plot.R
\docType{methods}
\name{Plot} \name{Plot}
\alias{Plot} \alias{Plot}
\alias{Plot,overlapped_genome_features-method} \alias{Plot,overlapped_genome_features-method}
......
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Table.R % Please edit documentation in R/Table.R
\docType{methods}
\name{Table} \name{Table}
\alias{Table} \alias{Table}
\alias{Table,overlapped_genome_features-method} \alias{Table,overlapped_genome_features-method}
......
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/build_genome_features.R % Please edit documentation in R/build_genome_features.R
\docType{methods}
\name{build_genome_features} \name{build_genome_features}
\alias{build_genome_features} \alias{build_genome_features}
\alias{build_genome_features,TxDb-method} \alias{build_genome_features,TxDb-method}
\title{build a convenient genomic features object.} \title{build a convenient genomic features object.}
\usage{ \usage{
build_genome_features(txdb, features = c("promoter", "UTR5", "UTR3", build_genome_features(
"exon", "intron", "cds", "downstream"), txdb,
parameters = list(promoter_ranges = list(upstream = 3000, downstream = features = c("promoter", "UTR5", "UTR3", "exon", "intron", "cds", "downstream"),
500), downstream_range = 1000)) parameters = list(promoter_ranges = list(upstream = 3000, downstream = 500),
downstream_range = 1000)
)
\S4method{build_genome_features}{TxDb}(txdb, features = c("promoter", \S4method{build_genome_features}{TxDb}(
"UTR5", "UTR3", "exon", "intron", "cds", "downstream"), txdb,
parameters = list(promoter_ranges = list(upstream = 3000, downstream = features = c("promoter", "UTR5", "UTR3", "exon", "intron", "cds", "downstream"),
500), downstream_range = 1000)) parameters = list(promoter_ranges = list(upstream = 3000, downstream = 500),
downstream_range = 1000)
)
} }
\arguments{ \arguments{
\item{txdb}{a txdb database built with \pkg{GenomicFeatures} (see example).} \item{txdb}{a txdb database built with \pkg{GenomicFeatures} (see example).}
......
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/genome_features_overlaps.R % Please edit documentation in R/genome_features_overlaps.R
\docType{methods}
\name{genome_features_overlaps} \name{genome_features_overlaps}
\alias{genome_features_overlaps} \alias{genome_features_overlaps}
\alias{genome_features_overlaps,CompressedGRangesList,genome_features-method} \alias{genome_features_overlaps,CompressedGRangesList,genome_features-method}
\title{find overlaps between genomic coordinates and features.} \title{find overlaps between genomic coordinates and features.}
\usage{ \usage{
genome_features_overlaps(peaks, features, figs_path = "./data/figs/", genome_features_overlaps(
ignore.strand = TRUE) peaks,
features,
figs_path = "./data/figs/",
ignore.strand = TRUE
)
\S4method{genome_features_overlaps}{CompressedGRangesList,genome_features}(peaks, \S4method{genome_features_overlaps}{CompressedGRangesList,genome_features}(
features, figs_path = "./data/figs/", ignore.strand = TRUE) peaks,
features,
figs_path = "./data/figs/",
ignore.strand = TRUE
)
} }
\arguments{ \arguments{
\item{peaks}{a \code{\link[base]{list}} of \code{\link[GenomicRanges]{GRanges}} objects elements provided by \code{\link{readPeakFile}}.} \item{peaks}{a \code{\link[base]{list}} of \code{\link[GenomicRanges]{GRanges}} objects elements provided by \code{\link{readPeakFile}}.}
\item{features}{a \code{\link{genome_features-class}} object.} \item{features}{a \code{\link{genome_features-class}} object.}
\item{figs_path}{the path where print the \code{\link[UpSetR]{upstet}} plots. ("./data/figs/", by default).} \item{figs_path}{the path where print the \code{\link[UpSetR]{upset}} plots. ("./data/figs/", by default).}
\item{ignore.strand}{ignore peak coordinate orientation (defaul to TRUE).} \item{ignore.strand}{ignore peak coordinate orientation (defaul to TRUE).}
} }
......
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