intersectWithFeature: Intersect the windows data frame with an annotation data...

Description Usage Arguments Value See Also Examples

View source: R/intersectWithFeature.R

Description

Intersect the windows with an annotation data frame to get features that overlap with each window

Usage

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intersectWithFeature(windows, annotation, getFeatureInfo = FALSE,
overlapCol = "OverlapFeature", mcolsAnnot, collapse, ...)

Arguments

windows

data frame containing the strand information of the sliding windows. Windows can be obtained using the function getWinFromBamFile.

annotation

a Grange object that you want to intersect with your windows. It can have mcols which contains the information or features that could be able to integrate to the input windows

getFeatureInfo

whether to get the information of features in the mcols of annotation data or not. If FALSE the return windows will have an additional column indicating whether a window overlaps with any range of the annotion data. If TRUE the return windows will contain the information of features that overlap each window

overlapCol

the columnn name of the return windows indicating whether a window overlaps with any range of the annotion data.

mcolsAnnot

the column names of the mcols of the annotation data that you want to get information

collapse

character which is used collapse multiple features that overlap with a same window into a string. If missing then we don't collapse them.

...

used to pass parameters to GenomicRanges::findOverlaps

Value

the input windows DataFrame with some additional columns

See Also

getWinFromBamFile, plotHist, plotWin

Examples

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bamfilein = system.file('extdata','s2.sorted.bam',package = 'strandCheckR')
windows <- getWinFromBamFile(file = bamfilein)
#add chr before chromosome names to be consistent with the annotation
windows$Seq <- paste0('chr',windows$Seq) 
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
annot <- transcripts(TxDb.Hsapiens.UCSC.hg38.knownGene)
# get the transcript names that overlap with each window
windows <- intersectWithFeature(windows,annot,mcolsAnnot='tx_name') 
# just want to know whether there's any transcript that 
# overlaps with each window
windows <- intersectWithFeature(windows,annot,overlapCol='OverlapTranscript')
plotHist(windows,facets = 'OverlapTranscript')
plotWin(windows,facets = 'OverlapTranscript')

strandCheckR documentation built on Nov. 1, 2018, 2:26 a.m.