Centromere base positions

Description

Centromere base positions from the GRCh36/hg18, GRCh37/hg19 and GRCh38/hg38 genome builds.

Usage

data(centromeres.hg18)
data(centromeres.hg19)
data(centromeres.hg38)

Format

A data frame with the following columns.

chrom

chromosome (1-22, X, Y)

left.base

starting base position of centromere

right.base

ending base position of centromere

Note

The UCSC genome browser lists two regions for the Y chromosome centromere in build hg18. We removed the positions (12208578, 12308578) from the centromere table to avoid problems with duplicate entries in the code.

Source

hg18 and hg19: UCSC genome browser (http://genome.ucsc.edu)

hg38: Genome Reference Consortium (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/).

Examples

data(centromeres.hg18)
data(centromeres.hg19)
data(centromeres.hg38)

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(GWASTools)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GWASTools/centromeres.Rd_%03d_medium.png", width=480, height=480)
> ### Name: centromeres
> ### Title: Centromere base positions
> ### Aliases: centromeres centromeres.hg18 centromeres.hg19 centromeres.hg38
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(centromeres.hg18)
> data(centromeres.hg19)
> data(centromeres.hg38)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>