doAnnotation: Annotate a GRanges object using one of annotation functions.

In hiAnnotator: Functions for annotating GRanges objects

Description

This is a wrapper function which calls one of following functions depending on annotType parameter: getFeatureCounts, getFeatureCountsBig, getNearestFeature, get2NearestFeature, getSitesInFeature

Usage

doAnnotation(annotType = NULL, ..., postProcessFun = NULL,
  postProcessFunArgs = list())

Arguments

annotType	one of following: within, nearest, twoNearest, counts, countsBig.
...	Additional parameters to be passed to the respective annotation function.
postProcessFun	function to call on the resulting object for any post processing steps.
postProcessFunArgs	additional arguments for postProcessFun as a list.

Value

a GRanges object with new annotation columns appended at the end of sites.rd.

See Also

makeGRanges, getFeatureCounts, getFeatureCountsBig, getNearestFeature, get2NearestFeature, getSitesInFeature.

Examples

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

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

doAnnotation(annotType = "within", alldata.rd, genes.rd, "InGene", asBool = TRUE)
## Not run: 
doAnnotation(annotType = "counts", alldata.rd, genes.rd, "NumOfGene")
doAnnotation(annotType = "nearest", alldata.rd, genes.rd, "NearestGene")
doAnnotation(annotType = "countsBig", alldata.rd, genes.rd, "ChipSeqCounts")
geneCheck <- function(x,wanted) { x$isWantedGene <- x$InGene %in% wanted;
return(x) }
doAnnotation(annotType = "within", alldata.rd, genes.rd, "InGene",
postProcessFun = geneCheck,
postProcessFunArgs = list("wanted" = c("FOXJ3", "SEPT9", "RPTOR")) )

## End(Not run)

hiAnnotator documentation built on Nov. 8, 2020, 7:27 p.m.