hiAnnotator: Functions for annotating GRanges objects

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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 <malnirav@gmail.com>
Date of publication
None
Maintainer
Nirav V Malani <malnirav@gmail.com>
License
GPL (>= 2)
Version
1.8.0

View on Bioconductor

Man pages

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

Files in this package

hiAnnotator/DESCRIPTION
hiAnnotator/NAMESPACE
hiAnnotator/NEWS
hiAnnotator/R
hiAnnotator/R/hiAnnotator.R
hiAnnotator/R/plotTypes.R
hiAnnotator/README.md
hiAnnotator/build
hiAnnotator/build/vignette.rds
hiAnnotator/data
hiAnnotator/data/genes.rda
hiAnnotator/data/sites.ctrl.rda
hiAnnotator/data/sites.rda
hiAnnotator/inst
hiAnnotator/inst/doc
hiAnnotator/inst/doc/Intro.R
hiAnnotator/inst/doc/Intro.Rmd
hiAnnotator/inst/doc/Intro.html
hiAnnotator/inst/tests
hiAnnotator/inst/tests/test_coreFeatures.R
hiAnnotator/man
hiAnnotator/man/cleanColname.Rd
hiAnnotator/man/doAnnotation.Rd
hiAnnotator/man/genes.Rd
hiAnnotator/man/get2NearestFeature.Rd
hiAnnotator/man/getFeatureCounts.Rd
hiAnnotator/man/getFeatureCountsBig.Rd
hiAnnotator/man/getLowestDists.Rd
hiAnnotator/man/getNearestFeature.Rd
hiAnnotator/man/getRelevantCol.Rd
hiAnnotator/man/getSitesInFeature.Rd
hiAnnotator/man/getUCSCtable.Rd
hiAnnotator/man/getWindowLabel.Rd
hiAnnotator/man/hiAnnotator.Rd
hiAnnotator/man/makeChunks.Rd
hiAnnotator/man/makeGRanges.Rd
hiAnnotator/man/makeUCSCsession.Rd
hiAnnotator/man/plotdisFeature.Rd
hiAnnotator/man/sites.Rd
hiAnnotator/man/sites.ctrl.Rd
hiAnnotator/tests
hiAnnotator/tests/runTests.R
hiAnnotator/vignettes
hiAnnotator/vignettes/Intro.Rmd
hiAnnotator/vignettes/figure
hiAnnotator/vignettes/figure/unnamed-chunk-9-1.png
hiAnnotator/vignettes/figure/unnamed-chunk-9-2.png
hiAnnotator/vignettes/figure/unnamed-chunk-9-3.png
hiAnnotator/vignettes/figure/unnamed-chunk-9-4.png