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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("hiAnnotator")
AuthorNirav V Malani <malnirav@gmail.com>
Bioconductor views Annotation Software
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

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

All documentation is copyright its authors; we didn't write any of that.