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Aurelien Brionne
GenomeFeatures
Commits
ddf5cc72
Commit
ddf5cc72
authored
Oct 16, 2020
by
Aurelien Brionne
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update
parent
c06a6116
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DESCRIPTION
View file @
ddf5cc72
...
@@ -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'
...
...
R/genome_features_overlaps.R
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ddf5cc72
...
@@ -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]{ups
t
et}} 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
()
})
})
...
...
man/Plot-methods.Rd
View file @
ddf5cc72
% 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}
...
...
man/Table-methods.Rd
View file @
ddf5cc72
% 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}
...
...
man/build_genome_features-methods.Rd
View file @
ddf5cc72
% 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).}
...
...
man/genome_features_overlaps-methods.Rd
View file @
ddf5cc72
% 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]{ups
t
et}} 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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