hiAnnotator: Functions for annotating GRanges objects

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.

AuthorNirav V Malani <malnirav@gmail.com>
Date of publicationNone
MaintainerNirav V Malani <malnirav@gmail.com>
LicenseGPL (>= 2)
Version1.8.0

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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

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