R: TSS annotation for human sapiens (GRCh37) obtained from...
TSS.human.GRCh37
R Documentation
TSS annotation for human sapiens (GRCh37) obtained from biomaRt
Description
TSS annotation for human sapiens (GRCh37) obtained from biomaRt
Usage
data(TSS.human.GRCh37)
Format
A GRanges object with slot start holding the start position of the gene,
slot end holding the end position of the gene, slot names holding ensembl
gene id, slot seqnames holding the chromosome location where the gene is
located and slot strand holding the strinad information. In addition, the
following variables are included.
description
description of the gene
Details
The dataset TSS.human.GRCh37 was obtained by:
mart = useMart(biomart = "ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org",
path="/biomart/martservice", dataset = "hsapiens_gene_ensembl")
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.
You are welcome to redistribute it under certain conditions.
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
'help.start()' for an HTML browser interface to help.
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/TSS.human.GRCh37.Rd_%03d_medium.png", width=480, height=480)
> ### Name: TSS.human.GRCh37
> ### Title: TSS annotation for human sapiens (GRCh37) obtained from biomaRt
> ### Aliases: TSS.human.GRCh37
> ### Keywords: datasets
>
> ### ** Examples
>
> data(TSS.human.GRCh37)
> slotNames(TSS.human.GRCh37)
[1] "seqnames" "ranges" "strand" "elementMetadata"
[5] "seqinfo" "metadata"
>
>
>
>
>
> dev.off()
null device
1
>