hiAnnotator (version 1.6.2)

getFeatureCounts: Get counts of annotation within a defined window around each query range or positions.

Description

Given a query object and window size(s), the function finds all the rows in subject which are <= 2="" window="" size="" distance="" away.="" if="" weights="" are="" assigned="" to="" each="" positions="" in="" the="" subject,="" then="" tallied="" counts="" multiplied="" accordingly.="" for="" large="" annotations,="" use="" getFeatureCountsBig.

Usage

getFeatureCounts(sites.rd, features.rd, colnam = NULL, chromSizes = NULL,
  widths = c(1000, 10000, 1e+06), weightsColname = NULL,
  doInChunks = FALSE, chunkSize = 10000, parallel = FALSE)

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!

chromSizes

named vector of chromosome/seqnames sizes to be used for testing if a position is off the mappable region. DEPRECATED and will be removed in future release.

widths

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

weightsColname

if defined, weigh each row from features.rd when tallying up the counts.

doInChunks

break up sites.rd into small pieces of chunkSize to perform the calculations. Default is FALSE. Useful if you are expecting to find great deal of overlap between sites.rd and features.rd.

chunkSize

number of rows to use per chunk of sites.rd. Default to 10000. Only used if doInChunks=TRUE.

parallel

use parallel backend to perform calculation with foreach. Defaults to FALSE. If no parallel backend is registered, then a serial version of foreach is ran using registerDoSEQ.

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, getFeatureCountsBig.

Examples

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

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

geneCounts <- getFeatureCounts(alldata.rd,genes.rd,"NumOfGene")
geneCounts <- getFeatureCounts(alldata.rd,genes.rd,"NumOfGene",
doInChunks=TRUE, chunkSize=200)
geneCounts
## Parallel version of getFeatureCounts
# geneCounts <- getFeatureCounts(alldata.rd,genes.rd,"NumOfGene",
parallel=TRUE)
# geneCounts