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

Description Usage Arguments Value See Also Examples

View source: R/hiAnnotator.R

Description

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

Usage

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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

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# 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)

malnirav/hiAnnotator documentation built on July 29, 2021, 6:32 a.m.