Functions for annotating GRanges objects

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Documentation for package ‘hiAnnotator’ version 1.43.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
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.checkArgsSetDefaults	Check args and set defaults.
.mergeAndReturn	Merge results back to the query object and perform additional post processing steps.
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