chrInfo-methods: Get chromosome start and stop positions

In genoset: A RangedSummarizedExperiment with methods for copy number analysis

Description

Provides a matrix of start, stop and offset, in base numbers for each chromosome.

Usage

chrInfo(object)

## S4 method for signature 'GenoSetOrGenomicRanges'
chrInfo(object)

Arguments

object

A GenoSet object or similar

Value

list with start and stop position, by ordered chr

Examples

  data(genoset,package='genoset')
  chrInfo(genoset.ds)
  chrInfo(rowRanges(genoset.ds))  # The same

Example output

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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply

Warning messages:
1: no function found corresponding to methods exports from 'DelayedArray' for: 'acbind', 'arbind' 
2: no function found corresponding to methods exports from 'SummarizedExperiment' for: 'acbind', 'arbind' 
3: multiple methods tables found for 'pos' 
          start      stop    offset
chr8          1 136970000         0
chr12 136970001 149937501 136970000
chr17 149937502 185907501 149937501
          start      stop    offset
chr8          1 136970000         0
chr12 136970001 149937501 136970000
chr17 149937502 185907501 149937501

genoset documentation built on Nov. 8, 2020, 6:07 p.m.