getBins

Description

Get uniformly-sized bins of specified width

Usage

getBins(chroms, ideo, binLim = NULL, stepSize)

Arguments

Details

This is a helper function used to generate binned data for plotOnIdeo(). It takes the chromosome-wide extents from ideo, which is essentially the cytoBandIdeo table from UCSC browser with the header as the first row. A use case is to generate bins using this function and supply the output to avgByBin() to bin the data.

Value

(GRanges) bin ranges in 1-base coordinates

Author(s)

Shraddha Pai <Shraddha.Pai@camh.ca>, Jingliang Ren

See Also

getIdeo(),avgByBin()

Examples

ideo_hg19 <- getIdeo("hg19")
chrom_bins <- getBins(c("chr1","chr2","chrX"), ideo_hg19,stepSize=5*100*1000)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(IdeoViz)
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")'.

Loading required package: IRanges
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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: RColorBrewer
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/IdeoViz/getBins.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getBins
> ### Title: getBins
> ### Aliases: getBins
> 
> ### ** Examples
> ideo_hg19 <- getIdeo("hg19")
Error in `genome<-`(`*tmp*`, value = "hg19") : 
  Failed to set session genome to 'hg19'
Calls: getIdeo -> genome<- -> genome<-
Execution halted