getFeatureCountsBig: Get counts of annotation within a defined window around each...
In hiAnnotator: Functions for annotating GRanges objects

Description Usage Arguments Value See Also Examples

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

1 2	getFeatureCountsBig(sites.rd, features.rd, colnam = NULL, widths = c(1000, 10000, 1e+06))

`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)`

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.

makeGRanges, getNearestFeature, getSitesInFeature, getFeatureCounts.

# 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")
## Not run: 
geneCounts2 <- getFeatureCountsBig(alldata.rd, genes.rd, "NumOfGene")
identical(geneCounts1, geneCounts2)

## End(Not run)