R: Gene model with exon, 5' UTR and 3' UTR information for human...
ExonPlusUtr.human.GRCh37
R Documentation
Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37)
obtained from biomaRt
Description
Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37)
obtained from biomaRt
Usage
data(ExonPlusUtr.human.GRCh37)
Format
RangedData with slot start holding the start position of the exon, slot end
holding the end position of the exon, slot rownames holding ensembl
transcript id and slot space holding the chromosome location where the gene
is located. In addition, the following variables are included.
strand
1 for positive strand and -1 for negative strand
description
description of the transcript
ensembl_gene_id
gene id
utr5start
5' UTR start
utr5end
5' UTR end
utr3start
3' UTR start
utr3end
3' UTR end
Details
used in the examples
Annotation data obtained by:
mart = useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
ExonPlusUtr.human.GRCh37 =
getAnnotation(mart=human, featureType="ExonPlusUtr")
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> library(ChIPpeakAnno)
Loading required package: grid
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: VennDiagram
Loading required package: futile.logger
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ChIPpeakAnno/ExonPlusUtr.human.GRCh37.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ExonPlusUtr.human.GRCh37
> ### Title: Gene model with exon, 5' UTR and 3' UTR information for human
> ### sapiens (GRCh37) obtained from biomaRt
> ### Aliases: ExonPlusUtr.human.GRCh37
> ### Keywords: datasets
>
> ### ** Examples
>
> data(ExonPlusUtr.human.GRCh37)
> slotNames(ExonPlusUtr.human.GRCh37)
[1] "ranges" "values" "elementType" "elementMetadata"
[5] "metadata"
>
>
>
>
>
> dev.off()
null device
1
>