1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
|
\name{getGeneRegionTrackForGviz}
\Rdversion{1.1}
\alias{getGeneRegionTrackForGviz}
\alias{getGeneRegionTrackForGviz,EnsDb-method}
\title{Utility functions}
\description{
Utility functions integrating \code{EnsDb} objects with other
Bioconductor packages.
}
\usage{
\S4method{getGeneRegionTrackForGviz}{EnsDb}(x,
filter = AnnotationFilterList(), chromosome = NULL,
start = NULL, end = NULL, featureIs = "gene_biotype")
}
\arguments{
(In alphabetic order)
\item{chromosome}{
For \code{getGeneRegionTrackForGviz}: optional chromosome name to
restrict the returned entry to a specific chromosome.
}
\item{end}{
For \code{getGeneRegionTrackForGviz}: optional chromosomal end
coordinate specifying, together with \code{start}, the chromosomal
region from which features should be retrieved.
}
\item{featureIs}{
For \code{getGeneRegionTrackForGviz}: whether the gene
(\code{"gene_biotype"}) or the transcript biotype
(\code{"tx_biotype"}) should be returned in column \code{"feature"}.
}
\item{filter}{
A filter describing which results to retrieve from the database. Can
be a single object extending
\code{\link[AnnotationFilter]{AnnotationFilter}}, an
\code{\link[AnnotationFilter]{AnnotationFilterList}} object
combining several such objects or a \code{formula} representing a
filter expression (see examples below or
\code{\link[AnnotationFilter]{AnnotationFilter}} for more details).
}
\item{start}{
For \code{getGeneRegionTrackForGviz}: optional chromosomal start
coordinate specifying, together with \code{end}, the chromosomal
region from which features should be retrieved.
}
\item{x}{
For \code{toSAF} a \code{GRangesList} object. For all other
methods an \code{EnsDb} instance.
}
}
\section{Methods and Functions}{
\describe{
\item{getGeneRegionTrackForGviz}{
Retrieve a \code{GRanges} object with transcript features from the
\code{EnsDb} that can be used directly in the \code{Gviz} package
to create a \code{GeneRegionTrack}. Using the \code{filter},
\code{chromosome}, \code{start} and \code{end} arguments it is
possible to fetch specific features (e.g. lincRNAs) from the
database.
If \code{chromosome}, \code{start} and \code{end} is provided the
function internally first retrieves all transcripts that have an
exon or an intron in the specified chromosomal region and
subsequently fetch all of these transcripts. This ensures that all
transcripts of the region are returned, even those that have
\emph{only} an intron in the region.
The function returns a \code{GRanges} object with additional
annotation columns \code{"feature"}, \code{"gene"}, \code{"exon"},
\code{"exon_rank"}, \code{"trancript"}, \code{"symbol"} specifying
the feature type (either gene or transcript biotype), the
(Ensembl) gene ID, the exon ID, the rank/index of the exon in the
transcript, the transcript ID and the gene symbol/name.
}
}
}
\value{
For \code{getGeneRegionTrackForGviz}: see method description above.
}
\author{
Johannes Rainer
}
\seealso{
\code{\link{transcripts}}
}
\examples{
library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86
###### getGeneRegionTrackForGviz
##
## Get all genes encoded on chromosome Y in the specifyed region.
AllY <- getGeneRegionTrackForGviz(edb, chromosome = "Y", start = 5131959,
end = 7131959)
## We could plot this now using plotTracks(GeneRegionTrack(AllY))
}
\keyword{classes}
|
