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

In UofABioinformaticsHub/strandCheckR: Calculate strandness information of a bam file

Description

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

Usage

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 getStrandFromBamFile.
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

getStrandFromBamFile, plotHist, plotWin

Examples

bamfilein = system.file('extdata','s2.sorted.bam',package = 'strandCheckR')
windows <- getStrandFromBamFile(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')

UofABioinformaticsHub/strandCheckR documentation built on Aug. 15, 2021, 9:08 a.m.