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Intersect the windows data frame with an annotation data frame

Source: R/intersectWithFeature.R
intersectWithFeature.Rd

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)
#> Testing paired end by checking the first 1e+05 reads of file /__w/_temp/Library/strandCheckR/extdata/s2.sorted.bam
#> Your bam file is single end
#> Reading file /__w/_temp/Library/strandCheckR/extdata/s2.sorted.bam
#> Read sequences 10
#add chr before chromosome names to be consistent with the annotation
windows$Seq <- paste0('chr',windows$Seq)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
#> Loading required package: GenomicFeatures
#> Loading required package: AnnotationDbi
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
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')
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_point()`).