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

View on Bioconductor

Functions

cleanColname Man page
doAnnotation Man page
genes Man page
get2NearestFeature Man page
getFeatureCounts Man page
getFeatureCountsBig Man page
getLowestDists Man page
getNearestFeature Man page
getRelevantCol Man page
getSitesInFeature Man page
getUCSCtable Man page
getWindowLabel Man page
hiAnnotator Man page
hiAnnotator-package Man page
makeChunks Man page
makeGRanges Man page
makeUCSCsession Man page
plotdisFeature Man page
sites Man page
sites.ctrl Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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