TSS annotation for human sapiens (NCBI36) obtained from biomaRt

Description

TSS annotation for human sapiens (NCBI36) obtained from biomaRt

Usage

data(TSS.human.NCBI36)

Format

GRanges 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

used in the examples Annotation data obtained by:

mart = useMart(biomart = "ensembl_mart_47", dataset = "hsapiens_gene_ensembl", archive=TRUE)

getAnnotation(mart, featureType = "TSS")

Examples

data(TSS.human.NCBI36)
slotNames(TSS.human.NCBI36)

Results

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.NCBI36.Rd_%03d_medium.png", width=480, height=480)
> ### Name: TSS.human.NCBI36
> ### Title: TSS annotation for human sapiens (NCBI36) obtained from biomaRt
> ### Aliases: TSS.human.NCBI36
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(TSS.human.NCBI36)
> slotNames(TSS.human.NCBI36)
[1] "seqnames"        "ranges"          "strand"          "elementMetadata"
[5] "seqinfo"         "metadata"       
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>