Functions for annotating GRanges objects

Documentation for package ‘hiAnnotator’ version 1.11.1

hiAnnotator-package	Annotating GRanges objects with hiAnnotator.
cleanColname	Clean the supplied string from punctuations and spaces.
doAnnotation	Annotate a GRanges object using one of annotation functions.
genes	Sample RefSeq genes annotation
get2NearestFeature	Get two nearest upstream and downstream annotation boundary for a position range.
getFeatureCounts	Get counts of annotation within a defined window around each query range or positions.
getFeatureCountsBig	Get counts of annotation within a defined window around each query range/position for large annotation objects spanning greater than 1 billion rows.
getLowestDists	Get the lowest biological distance from the 5' or 3' boundaries of query and subject.
getNearestFeature	Get nearest annotation boundary for a position range.
getRelevantCol	Find the column index of interest given the potential choices.
getSitesInFeature	Find overlapping positions/ranges that match between the query and subject.
getUCSCtable	Obtain a UCSC annotation table given the table & track name.
getWindowLabel	Generate a window size label.
hiAnnotator	Annotating GRanges objects with hiAnnotator.
makeChunks	Breaks two GRanges objects into chunks of N size.
makeGRanges	Make a sorted GRanges object from a dataframe.
makeUCSCsession	Initiate UCSC genome browser session given the freeze argument.
plotdisFeature	Plot distance distribution to a feature boundary.
sites	Sample Retrovirus Integration Sites data
sites.ctrl	Controls for Sample Retrovirus Integration Sites data