hiAnnotator contains set of functions which allow users to annotate a GRanges object with custom set of annotations. The basic philosophy of this package is to take two GRanges objects (query & subject) with common set of seqnames (i.e. chromosomes) and return associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands). The package comes with three types of annotation functions which calculates if a position from query is: within a feature, near a feature, or count features in defined window sizes. Moreover, each function is equipped with parallel backend to utilize the foreach package. In addition, the package is equipped with wrapper functions, which finds appropriate columns needed to make a GRanges object from a common data frame.
|Author||Nirav V Malani <firstname.lastname@example.org>|
|Date of publication||None|
|Maintainer||Nirav V Malani <email@example.com>|
|License||GPL (>= 2)|
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...
getFeatureCounts: Get counts of annotation within a defined window around each...
getFeatureCountsBig: Get counts of annotation within a defined window around each...
getLowestDists: Get the lowest biological distance from the 5' or 3'...
getNearestFeature: Get nearest annotation boundary for a position range.
getRelevantCol: Find the column index of interest given the potential...
getSitesInFeature: Find overlapping positions/ranges that match between the...
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...
plotdisFeature: Plot distance distribution to a feature boundary.
sites: Sample Retrovirus Integration Sites data
sites.ctrl: Controls for Sample Retrovirus Integration Sites data