# Functions for annotating GRanges objects

## Documentation for package ‘hiAnnotator’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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