getBins: getBins

In shraddhapai/IdeoViz: Plots data (continuous/discrete) along chromosomal ideogram

Description

getBins

Usage

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

Arguments

chroms	(character) chromosomes to generate bins for
ideo	(data.frame) ideogram table as generated by getIdeo(). See that function for details.
stepSize	(integer) bin size in bases
binLim	(numeric,

length 2) [start, end] of genomic range to generate bins for. A value of NULL results in binning of entire chromosome

Details

Get uniformly-sized bins of specified width 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

See Also

getIdeo(),avgByBin()

Examples

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

shraddhapai/IdeoViz documentation built on April 27, 2020, 10:36 p.m.