hiAnnotator (version 1.6.2)

getFeatureCountsBig: Get counts of annotation within a defined window around each query range/position for large annotation objects spanning greater than 1 billion rows.

Description

Given a query object and window size(s), the function finds all the rows in subject which are <= 2="" window="" size="" distance="" away.="" note="" that="" here="" counting="" is="" done="" using="" midpoint="" of="" the="" ranges="" in="" query="" instead="" start-stop="" boundaries.="" counts="" will="" differ="" slightly="" when="" compared="" to="" getFeatureCounts.

Usage

getFeatureCountsBig(sites.rd, features.rd, colnam = NULL, widths = c(1000,
  10000, 1e+06))

Arguments

sites.rd

GRanges object to be used as the query.

features.rd

GRanges object to be used as the subject or the annotation table.

colnam

column name to be added to sites.rd for the newly calculated annotation...serves as a prefix to windows sizes!

widths

a named/numeric vector of window sizes to be used for casting a net around each position. Default: c(1000,10000,1000000)

Value

• a GRanges object with new annotation columns appended at the end of sites.rd. There will be a column for each width defined in widths parameter. If widths was a named vector i.e. c("100bp"=100,"1K"=1000), then the colname parameter will be pasted together with width name else default name will be generated by the function.

See Also

makeGRanges, getNearestFeature, getSitesInFeature, getFeatureCounts.

Examples

# Convert a dataframe to GRanges object
data(sites)
alldata.rd <- makeGRanges(sites,soloStart=TRUE)

data(genes)
genes.rd <- makeGRanges(genes)

geneCounts1 <- getFeatureCounts(alldata.rd,genes.rd,"NumOfGene")
geneCounts2 <- getFeatureCountsBig(alldata.rd,genes.rd,"NumOfGene")
identical(geneCounts1,geneCounts2)