HDF5Array: An array-like container for convenient access and manipulation of HDF5 datasets

This package implements the HDF5Array class for convenient access and manipulation of HDF5 datasets. In order to reduce memory usage and optimize performance, operations on an HDF5Array object are either delayed or executed using a block processing mechanism. The delaying and block processing mechanisms are independent of the on-disk backend and implemented via the DelayedArray class. They even work on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, or ordinary arrays or data frames, where they can improve performance.

AuthorHervé Pagès
Date of publicationNone
MaintainerHervé Pagès <hpages@fredhutch.org>
LicenseArtistic-2.0
Version1.2.1

View on Bioconductor

Functions

\%*\% Man page
acbind Man page
acbind,DelayedArray-method Man page
anyNA,DelayedArray-method Man page
apply Man page
apply,DelayedArray-method Man page
arbind Man page
arbind,DelayedArray-method Man page
as.array.DelayedArray Man page
as.array,DelayedArray-method Man page
as.data.frame.DelayedArray Man page
as.data.frame,DelayedArray-method Man page
as.matrix.DelayedArray Man page
as.matrix,DelayedArray-method Man page
as.vector.DelayedArray Man page
as.vector,DelayedArray-method Man page
cbind Man page
cbind,DelayedArray-method Man page
cbind,DelayedMatrix-method Man page
cbind-methods Man page
c,DelayedArray-method Man page
class:DelayedArray Man page
class:DelayedMatrix Man page
class:HDF5Array Man page
class:HDF5Dataset Man page
class:HDF5Matrix Man page
coerce,DelayedArray,DelayedMatrix-method Man page
coerce,DelayedArray,HDF5Array-method Man page
coerce,DelayedArray,HDF5Matrix-method Man page
coerce,DelayedMatrix,HDF5Matrix-method Man page
coerce,HDF5Array,HDF5Matrix-method Man page
colMeans Man page
colMeans,DelayedMatrix-method Man page
colSums Man page
colSums,DelayedMatrix-method Man page
DelayedArray Man page
DelayedArray-class Man page
!,DelayedArray-method Man page
[,DelayedArray-method Man page
[[,DelayedArray-method Man page
-,DelayedArray,missing-method Man page
+,DelayedArray,missing-method Man page
DelayedArray-utils Man page
DelayedMatrix Man page
DelayedMatrix-class Man page
\%*\%,DelayedMatrix,DelayedMatrix-method Man page
\%*\%,DelayedMatrix,matrix-method Man page
dim,ConformableSeedCombiner-method Man page
dim<-,DelayedArray-method Man page
dim,DelayedArray-method Man page
dim,HDF5Dataset-method Man page
dimnames,ConformableSeedCombiner-method Man page
dimnames<-,DelayedArray-method Man page
dimnames,DelayedArray-method Man page
dimnames,SeedBinder-method Man page
dim,SeedBinder-method Man page
drop,DelayedArray-method Man page
getHDF5DumpFile Man page
getHDF5DumpName Man page
HDF5Array Man page
HDF5Array-class Man page
HDF5Dataset Man page
HDF5Dataset-class Man page
HDF5Matrix Man page
HDF5Matrix-class Man page
isEmpty,DelayedArray-method Man page
is.finite,DelayedArray-method Man page
is.infinite,DelayedArray-method Man page
is.na,DelayedArray-method Man page
is.nan,DelayedArray-method Man page
length,ArrayBlocks-method Man page
length,DelayedArray-method Man page
lsHDF5DumpFile Man page
\%*\%,matrix,DelayedMatrix-method Man page
mean.DelayedArray Man page
mean,DelayedArray-method Man page
names<-,DelayedArray-method Man page
names,DelayedArray-method Man page
nchar,DelayedArray-method Man page
pmax2 Man page
pmax2,ANY,ANY-method Man page
pmax2,DelayedArray,DelayedArray-method Man page
pmax2,DelayedArray,vector-method Man page
pmax2,vector,DelayedArray-method Man page
pmin2 Man page
pmin2,ANY,ANY-method Man page
pmin2,DelayedArray,DelayedArray-method Man page
pmin2,DelayedArray,vector-method Man page
pmin2,vector,DelayedArray-method Man page
rbind Man page
rbind,DelayedArray-method Man page
rbind,DelayedMatrix-method Man page
round,DelayedArray-method Man page
rowMeans Man page
rowMeans,DelayedMatrix-method Man page
rowSums Man page
rowSums,DelayedMatrix-method Man page
setHDF5DumpFile Man page
setHDF5DumpName Man page
show,DelayedArray-method Man page
signif,DelayedArray-method Man page
splitAsList,DelayedArray-method Man page
split.DelayedArray Man page
split,DelayedArray,ANY-method Man page
t,DelayedArray-method Man page
tolower,DelayedArray-method Man page
toupper,DelayedArray-method Man page
which,DelayedArray-method Man page
writeHDF5Dataset Man page

Files

HDF5Array/DESCRIPTION
HDF5Array/NAMESPACE
HDF5Array/NOTES
HDF5Array/R
HDF5Array/R/DelayedArray-class.R HDF5Array/R/DelayedArray-stats.R HDF5Array/R/DelayedArray-utils.R HDF5Array/R/DelayedMatrix-utils.R HDF5Array/R/HDF5Array-class.R HDF5Array/R/block_processing.R HDF5Array/R/cbind-methods.R HDF5Array/R/setHDF5DumpFile.R HDF5Array/R/show-utils.R HDF5Array/R/utils.R HDF5Array/R/zzz.R
HDF5Array/TODO
HDF5Array/inst
HDF5Array/inst/extdata
HDF5Array/inst/extdata/toy.h5
HDF5Array/inst/unitTests
HDF5Array/inst/unitTests/test_DelayedArray-class.R
HDF5Array/inst/unitTests/test_DelayedArray-utils.R
HDF5Array/inst/unitTests/test_DelayedMatrix-utils.R
HDF5Array/inst/unitTests/test_HDF5Array-class.R
HDF5Array/inst/unitTests/test_block_processing.R
HDF5Array/inst/unitTests/test_cbind-methods.R
HDF5Array/man
HDF5Array/man/DelayedArray-class.Rd HDF5Array/man/DelayedArray-utils.Rd HDF5Array/man/HDF5Array-class.Rd HDF5Array/man/cbind-methods.Rd HDF5Array/man/setHDF5DumpFile.Rd
HDF5Array/tests
HDF5Array/tests/run_unitTests.R

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