GenomicFiles: Distributed computing by file or by range

This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicFiles")
AuthorBioconductor Package Maintainer [aut, cre], Valerie Obenchain [aut], Michael Love [aut], Lori Shepherd [aut], Martin Morgan [aut]
Bioconductor views Coverage DataImport Genetics Infrastructure Sequencing
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.12.0

View on Bioconductor

Functions

assay,RangedVcfStack,ANY-method Man page
assay,VcfStack,ANY-method Man page
class:GenomicFiles Man page
class:VcfStack Man page
colData<-,GenomicFiles,DataFrame-method Man page
colData<-,VcfStack,DataFrame-method Man page
colData,VcfStack-method Man page
colnames,VcfStack-method Man page
dimnames<-,GenomicFiles,list-method Man page
dimnames,VcfStack-method Man page
dim,VcfStack-method Man page
files Man page
files<- Man page
files<-,GenomicFiles,character-method Man page
files<-,GenomicFiles,List-method Man page
files,GenomicFiles-method Man page
files<-,VcfStack,character-method Man page
files,VcfStack-method Man page
files<-,VcfStack,VcfFileList-method Man page
files<-,VcfStack,VcfFile-method Man page
findTypeRegistry Man page
GenomicFiles Man page
[,GenomicFiles,ANY,ANY,ANY-method Man page
[,GenomicFiles,ANY,ANY-method Man page
GenomicFiles-class Man page
GenomicFiles-deprecated Man page
GenomicFiles,GenomicRangesORGRangesList,character-method Man page
GenomicFiles,GenomicRangesORGRangesList,list-method Man page
GenomicFiles,GenomicRangesORGRangesList,List-method Man page
GenomicFiles,missing,ANY-method Man page
GenomicFiles,missing,missing-method Man page
getVCFPath Man page
isPacked Man page
makeFileType Man page
pack Man page
pack,GRanges-method Man page
paths1kg Man page
RangedVcfStack Man page
[,RangedVcfStack,ANY,ANY,ANY-method Man page
[,RangedVcfStack,ANY,ANY-method Man page
RangedVcfStack-class Man page
readVcfStack Man page
reduceByFile Man page
reduceByFile,GenomicFiles,missing-method Man page
reduceByFile,GRanges,ANY-method Man page
reduceByFile,GRangesList,ANY-method Man page
reduceByRange Man page
reduceByRange,GenomicFiles,missing-method Man page
reduceByRange,GRanges,ANY-method Man page
reduceByRange,GRangesList,ANY-method Man page
reduceByYield Man page
reduceFiles Man page
reduceRanges Man page
REDUCEsampler Man page
registerFileType Man page
registry-utils Man page
rownames,VcfStack-method Man page
rowRanges<-,RangedVcfStack,GRanges-method Man page
rowRanges,RangedVcfStack-method Man page
seqinfo<-,RangedVcfStack-method Man page
seqinfo<-,VcfStack-method Man page
seqinfo,VcfStack-method Man page
seqlevelsStyle<-,RangedVcfStack-method Man page
seqlevelsStyle<-,VcfStack-method Man page
show,GenomicFiles-method Man page
show,VcfStack-method Man page
unpack Man page
unpack,list,GRangesList-method Man page
unpack,List,GRangesList-method Man page
VcfStack Man page
[,VcfStack,ANY,ANY,ANY-method Man page
[,VcfStack,ANY,ANY-method Man page
VcfStack-class Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/GenomicFiles-class.R R/VcfStack-class.R R/pack-methods.R R/reduceByFile-methods.R R/reduceByRange-methods.R R/reduceByYield.R R/reduceFiles.R R/reduceRanges.R R/registry.R R/unpack-methods.R R/zzz.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/GenomicFiles.R
inst/doc/GenomicFiles.Rnw
inst/doc/GenomicFiles.pdf
inst/extdata
inst/extdata/CEUtrio_11.vcf.bgz
inst/extdata/CEUtrio_11.vcf.bgz.tbi
inst/extdata/CEUtrio_20.vcf.bgz
inst/extdata/CEUtrio_20.vcf.bgz.tbi
inst/extdata/CEUtrio_21.vcf.bgz
inst/extdata/CEUtrio_21.vcf.bgz.tbi
inst/extdata/CEUtrio_22.vcf.bgz
inst/extdata/CEUtrio_22.vcf.bgz.tbi
inst/extdata/CEUtrio_7.vcf.bgz
inst/extdata/CEUtrio_7.vcf.bgz.tbi
inst/extdata/CEUtrio_X.vcf.bgz
inst/extdata/CEUtrio_X.vcf.bgz.tbi
inst/extdata/CEUtrio_Y.vcf.bgz
inst/extdata/CEUtrio_Y.vcf.bgz.tbi
inst/extdata/seqinfo.rds
inst/scripts
inst/scripts/methods-FileManager.R
inst/unitTests
inst/unitTests/test_GenomicFiles-class.R inst/unitTests/test_VcfStack-class.R inst/unitTests/test_pack-methods.R inst/unitTests/test_reduceByFile-methods.R inst/unitTests/test_reduceByRange-methods.R
man
man/GenomicFiles-class.Rd man/GenomicFiles-deprecated.Rd man/VcfStack-class.Rd man/pack-methods.Rd man/reduceByFile-methods.Rd man/reduceByRange-methods.Rd man/reduceByYield.Rd man/registry-utils.Rd man/unpack-methods.Rd
tests
tests/GenomicFiles_unit_tests.R
vignettes
vignettes/GenomicFiles.Rnw
vignettes/reduceByFile_flow.png
vignettes/reduceByRange_flow.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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