h5vc: Managing alignment tallies using a hdf5 backend
Version 2.10.0

This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.

AuthorPaul Theodor Pyl
Date of publicationNone
MaintainerPaul Theodor Pyl <paul.theodor.pyl@gmail.com>
LicenseGPL (>= 3)
Version2.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("h5vc")

Getting started

Package overview

Popular man pages

getSampleData: Reading and writing sample data from / to a tally file
mergeTallyFiles: Merging multiple tally files into one
mismatchPlot: mismatchPlot
mutationSpectrum: Mutation spectrum analyses
plotMutationSpectrum: Plotting a mutation spectrum
prepareForHDF5: Preparing the results of tallyBAM for writing to an HDF5...
prepareTallyFile: prepareTallyFile
See all...

All man pages Function index File listing

Man pages

applyTallies: Preparing the results of tallyBAM for writing to an HDF5...
batchTallies: Tallying bam files in parallel using 'BatchJobs' on high...
binGenome: Function for binning a genome.
binnedAFs: Estimate allelic frequency distributions in bins along the...
callVariants: Variant calling
callVariantsFisher: Paired variant calling using fisher tests
callVariantsSingle: Single sample variant calling
coverage: Coverage analysis
geom_h5vc: geom_h5vc
getSampleData: Reading and writing sample data from / to a tally file
h5dapply: h5dapply
h5readBlock: h5readBlock
h5vc-package: Managing alignment tallies using a hdf5 backend
helpers: helper functions
mergeTallies: Merging the prepared results from multiple bam file tallies...
mergeTallyFiles: Merging multiple tally files into one
mismatchPlot: mismatchPlot
mutationSpectrum: Mutation spectrum analyses
plotMutationSpectrum: Plotting a mutation spectrum
prepareForHDF5: Preparing the results of tallyBAM for writing to an HDF5...
prepareTallyFile: prepareTallyFile
tallyBAM: tallyBAM
tallyRanges: Tallying function with a 'GRanges' interface.
writeReference: Filling the Reference dataset in a tally file from a...
writeToTallyFile: Writing data to an HDF5 tally file

Functions

applyTallies Man page Source code
bases Man page
batchTallies Man page Source code
batchTallyParam Man page Source code
binGenome Man page Source code
binnedAFs Man page Source code
binnedCoverage Man page Source code
blockify Source code
callDeletionsPaired Man page
callVariantsPaired Man page Source code
callVariantsPairedFisher Man page Source code
callVariantsSingle Man page Source code
collectTallies Man page Source code
defineBlocks Man page Source code
encodeDNAString Man page Source code
formatGenomicPosition Man page Source code
geom_h5vc Man page Source code
getChromSize Man page Source code
getDimensions Source code
getSampleData Man page Source code
h5dapply Man page
h5dapply,GRanges-method Man page
h5dapply,IRanges-method Man page
h5dapply,numeric-method Man page
h5dapplyIRanges Source code
h5readBlock Man page Source code
h5vc Man page
h5vc-package Man page
mergeByGene Source code
mergeTallies Man page Source code
mergeTallyFiles Man page Source code
mismatchPlot Man page Source code
mutationSpectrum Man page Source code
plotMutationSpectrum Man page Source code
prepareForHDF5 Man page Source code
prepareTallyFile Man page Source code
processDataForMismatchPlot Source code
rerunBatchTallies Man page Source code
resizeCohort Man page Source code
resubmitProblematicJobs Source code
setSampleData Man page Source code
setUpJobs Source code
tallyBAM Man page Source code
tallyRanges Man page Source code
tallyRangesBatch Man page Source code
tallyRangesToFile Man page Source code
variantCalls Man page
vcConfParams Man page Source code
waitAndCollect Source code
writeReference Man page Source code
writeToTallyFile Man page Source code Source code

Files

DESCRIPTION
NAMESPACE
R
R/applyTallies.R
R/call.variants.R
R/call.variants.fisher.R
R/call.variants.single.R
R/coverage.R
R/get.sample.metadata.R
R/getChromSize.R
R/h5apply.R
R/h5readBlock.R
R/helpers.R
R/mergeTallyFiles.r
R/mutation.spectrum.R
R/plotting.R
R/prepareForHDF5.R
R/prepareTallyFile.R
R/set.sample.metadata.R
R/tally.in.ranges.r
R/tallyBAM.R
R/write.reference.R
build
build/vignette.rds
data
data/bases.rda
inst
inst/CITATION
inst/doc
inst/doc/bioc_adapted.css
inst/doc/h5vc.simple.genome.browser.R
inst/doc/h5vc.simple.genome.browser.Rmd
inst/doc/h5vc.simple.genome.browser.html
inst/doc/h5vc.tour.R
inst/doc/h5vc.tour.Rmd
inst/doc/h5vc.tour.html
inst/extdata
inst/unitTests
inst/unitTests/expected.counts.txt
inst/unitTests/insert.bam
inst/unitTests/insert.bam.bai
inst/unitTests/test_tallyBAM.R
man
man/applyTallies.Rd
man/batchTallies.Rd
man/binGenome.Rd
man/binnedAFs.Rd
man/callVariants.Rd
man/callVariantsFisher.Rd
man/callVariantsSingle.Rd
man/coverage.Rd
man/geom_h5vc.Rd
man/getSampleData.Rd
man/h5dapply.Rd
man/h5readBlock.Rd
man/h5vc-package.Rd
man/helpers.Rd
man/mergeTallies.Rd
man/mergeTallyFiles.Rd
man/mismatchPlot.Rd
man/mutationSpectrum.Rd
man/plotMutationSpectrum.Rd
man/prepareForHDF5.Rd
man/prepareTallyFile.Rd
man/tallyBAM.Rd
man/tallyRanges.Rd
man/writeReference.Rd
man/writeToTallyFile.Rd
src
src/Makevars
src/Makevars.common
src/Makevars.win
src/tallyBAM.cpp
tests
tests/runTests.R
vignettes
vignettes/bioc_adapted.css
vignettes/example.plot.1.png
vignettes/example.plot.2.png
vignettes/example.plot.3.png
vignettes/example.plot.4.png
vignettes/example.plot.5.png
vignettes/h5vc.simple.genome.browser.Rmd
vignettes/h5vc.tour.Rmd
vignettes/mutation.spectrum.example.png
vignettes/tally.file.layout.png
h5vc documentation built on May 20, 2017, 10:24 p.m.

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