Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Aurelien Brionne
GenomeFeatures
Commits
ed786dfb
Commit
ed786dfb
authored
Dec 14, 2020
by
Aurelien Brionne
Browse files
intron1 adding
parent
e0f5d3c7
Changes
7
Hide whitespace changes
Inline
Side-by-side
DESCRIPTION
View file @
ed786dfb
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
View file @
ed786dfb
...
...
@@ -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
View file @
ed786dfb
...
...
@@ -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
View file @
ed786dfb
...
...
@@ -17,6 +17,7 @@ setClass("genome_features",
UTR5
=
"list"
,
exon
=
"list"
,
intron
=
"list"
,
intron1
=
"list"
,
cds
=
"list"
,
UTR3
=
"list"
,
downstream
=
"list"
,
...
...
README.md
View file @
ed786dfb
...
...
@@ -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
View file @
ed786dfb
...
...
@@ -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
View file @
ed786dfb
...
...
@@ -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
)
}
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment