Functions for annotating GRanges objects


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Documentation for package ‘hiAnnotator’ version 1.30.0

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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