Package: hiAnnotator 1.39.0

Nirav V Malani

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.

Authors:Nirav V Malani <[email protected]>

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hiAnnotator.pdf |hiAnnotator.html✨
hiAnnotator/json (API)
NEWS

# Install 'hiAnnotator' in R:
install.packages('hiAnnotator', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • genes - Sample RefSeq genes annotation
  • sites - Sample Retrovirus Integration Sites data
  • sites.ctrl - Controls for Sample Retrovirus Integration Sites data

On BioConductor:hiAnnotator-1.39.0(bioc 3.20)hiAnnotator-1.38.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

15 exports 1.08 score 80 dependencies 1 dependents

Last updated 2 months agofrom:946eaa3d56

Exports:cleanColnamedoAnnotationget2NearestFeaturegetFeatureCountsgetFeatureCountsBiggetLowestDistsgetNearestFeaturegetRelevantColgetSitesInFeaturegetUCSCtablegetWindowLabelmakeChunksmakeGRangesmakeUCSCsessionplotdisFeature

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeclicodetoolscolorspacecpp11crayoncurlDelayedArraydplyrfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc

Using hiAnnotator

Rendered fromIntro.Rmdusingknitr::knitron Jun 30 2024.

Last update: 2021-07-27
Started: 2014-04-14

Readme and manuals

Help Manual

Help pageTopics
Check args and set defaults..checkArgsSetDefaults
Merge results back to the query object and perform additional post processing steps..mergeAndReturn
Clean the supplied string from punctuations and spaces.cleanColname
Annotate a GRanges object using one of annotation functions.doAnnotation
Sample RefSeq genes annotationgenes
Get two nearest upstream and downstream annotation boundary for a position range.get2NearestFeature
Get counts of annotation within a defined window around each query range or positions.getFeatureCounts
Get counts of annotation within a defined window around each query range/position for large annotation objects spanning greater than 1 billion rows.getFeatureCountsBig
Get the lowest biological distance from the 5' or 3' boundaries of query and subject.getLowestDists
Get nearest annotation boundary for a position range.getNearestFeature
Find the column index of interest given the potential choices.getRelevantCol
Find overlapping positions/ranges that match between the query and subject.getSitesInFeature
Obtain a UCSC annotation table given the table & track name.getUCSCtable
Generate a window size label.getWindowLabel
Annotating GRanges objects with hiAnnotator.hiAnnotator
Breaks two GRanges objects into chunks of N size.makeChunks
Make a sorted GRanges object from a dataframe.makeGRanges
Initiate UCSC genome browser session given the freeze argument.makeUCSCsession
Plot distance distribution to a feature boundary.plotdisFeature
Sample Retrovirus Integration Sites datasites
Controls for Sample Retrovirus Integration Sites datasites.ctrl