centromeres: Centromere base positions

In GWASTools: Tools for Genome Wide Association Studies

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)

Example output

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, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

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

GWASTools documentation built on Nov. 8, 2020, 7:49 p.m.