A unified framework for working transparently with on-disk and in-memory array-like datasets


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Documentation for package ‘DelayedArray’ version 0.20.0

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A B C D E G I L M N P Q R S T U V W misc

-- A --

acbind Bind arrays along their rows or columns
acbind-method Common operations on DelayedArray objects
acbind-method Bind arrays along their rows or columns
all-method Operate natively on SparseArraySeed objects
any-method Operate natively on SparseArraySeed objects
anyNA-method Common operations on DelayedArray objects
anyNA-method Operate natively on SparseArraySeed objects
aperm DelayedArray objects
aperm-method ArrayGrid and ArrayViewport objects
aperm-method DelayedArray objects
aperm-method SparseArraySeed objects
aperm.ArbitraryArrayGrid ArrayGrid and ArrayViewport objects
aperm.DelayedArray DelayedArray objects
aperm.DummyArrayGrid ArrayGrid and ArrayViewport objects
aperm.RegularArrayGrid ArrayGrid and ArrayViewport objects
aperm.SparseArraySeed SparseArraySeed objects
apply Common operations on DelayedArray objects
apply-method Common operations on DelayedArray objects
arbind Bind arrays along their rows or columns
arbind-method Common operations on DelayedArray objects
arbind-method Bind arrays along their rows or columns
ArbitraryArrayGrid ArrayGrid and ArrayViewport objects
ArbitraryArrayGrid-class ArrayGrid and ArrayViewport objects
array selection Manipulation of array selections
array selections Manipulation of array selections
ArrayGrid ArrayGrid and ArrayViewport objects
ArrayGrid-class ArrayGrid and ArrayViewport objects
arrayRealizationSink-class Write blocks of data to a RealizationSink
ArrayViewport ArrayGrid and ArrayViewport objects
ArrayViewport-class ArrayGrid and ArrayViewport objects
array_selection Manipulation of array selections
array_selections Manipulation of array selections
as.array-method SparseArraySeed objects
as.array.SparseArraySeed SparseArraySeed objects
as.character-method ArrayGrid and ArrayViewport objects
as.character.ArrayGrid ArrayGrid and ArrayViewport objects
as.matrix-method SparseArraySeed objects
as.matrix.SparseArraySeed SparseArraySeed objects
AutoBlock-global-settings Control the geometry of automatic blocks
AutoGrid Create automatic grids to use for block processing of array-like objects
AutoRealizationSink Write blocks of data to a RealizationSink

-- B --

bind arrays Bind arrays along their rows or columns
bind-arrays Bind arrays along their rows or columns
bindROWS-method Common operations on DelayedArray objects
block processing blockApply() and family
blockApply blockApply() and family
blockGrid Create automatic grids to use for block processing of array-like objects
blockReduce blockApply() and family
block_processing blockApply() and family
BLOCK_write_to_sink Realize a DelayedArray object

-- C --

c-method DelayedArray objects
capped_volume_boxes Utilities to make capped volume boxes
cbind Common operations on DelayedArray objects
cbind-method Common operations on DelayedArray objects
cbind-method Operate natively on SparseArraySeed objects
ChunkedRleArraySeed RleArraySeed objects
ChunkedRleArraySeed-class RleArraySeed objects
class:ArbitraryArrayGrid ArrayGrid and ArrayViewport objects
class:ArrayGrid ArrayGrid and ArrayViewport objects
class:arrayRealizationSink Write blocks of data to a RealizationSink
class:ArrayViewport ArrayGrid and ArrayViewport objects
class:ChunkedRleArraySeed RleArraySeed objects
class:ConstantArray A DelayedArray subclass that contains a constant value
class:ConstantArraySeed A DelayedArray subclass that contains a constant value
class:ConstantMatrix A DelayedArray subclass that contains a constant value
class:DelayedAbind DelayedAbind objects
class:DelayedAperm DelayedAperm objects
class:DelayedArray DelayedArray objects
class:DelayedArray1 DelayedArray objects
class:DelayedMatrix DelayedArray objects
class:DelayedNaryIsoOp DelayedNaryIsoOp objects
class:DelayedNaryOp DelayedOp objects
class:DelayedOp DelayedOp objects
class:DelayedSetDimnames DelayedSetDimnames objects
class:DelayedSubassign DelayedSubassign objects
class:DelayedSubset DelayedSubset objects
class:DelayedUnaryIsoOp DelayedOp objects
class:DelayedUnaryIsoOpStack DelayedUnaryIsoOpStack objects
class:DelayedUnaryIsoOpWithArgs DelayedUnaryIsoOpWithArgs objects
class:DelayedUnaryOp DelayedOp objects
class:DummyArrayGrid ArrayGrid and ArrayViewport objects
class:DummyArrayViewport ArrayGrid and ArrayViewport objects
class:RealizationSink Write blocks of data to a RealizationSink
class:RegularArrayGrid ArrayGrid and ArrayViewport objects
class:RleArray RleArray objects
class:RleArraySeed RleArraySeed objects
class:RleMatrix RleArray objects
class:RleRealizationSink RleArraySeed objects
class:SafeArrayViewport ArrayGrid and ArrayViewport objects
class:SolidRleArraySeed RleArraySeed objects
class:SparseArraySeed SparseArraySeed objects
classNameForDisplay-method ArrayGrid and ArrayViewport objects
close-method Write blocks of data to a RealizationSink
coerce-method A DelayedArray subclass that contains a constant value
coerce-method DelayedArray objects
coerce-method RleArray objects
coerce-method RleArraySeed objects
coerce-method SparseArraySeed objects
coerce-method Write blocks of data to a RealizationSink
colAutoGrid Create automatic grids to use for block processing of array-like objects
colGrid Create automatic grids to use for block processing of array-like objects
colMaxs DelayedMatrix row/col summarization
colMaxs-method DelayedMatrix row/col summarization
colMeans DelayedMatrix row/col summarization
colMeans-method DelayedMatrix row/col summarization
colMins DelayedMatrix row/col summarization
colMins-method DelayedMatrix row/col summarization
colRanges DelayedMatrix row/col summarization
colRanges-method DelayedMatrix row/col summarization
colsum Common operations on DelayedMatrix objects
colsum-method Common operations on DelayedMatrix objects
colsum-method sparseMatrix utilities
colSums DelayedMatrix row/col summarization
colSums-method DelayedMatrix row/col summarization
ConstantArray A DelayedArray subclass that contains a constant value
ConstantArray-class A DelayedArray subclass that contains a constant value
ConstantArraySeed A DelayedArray subclass that contains a constant value
ConstantArraySeed-class A DelayedArray subclass that contains a constant value
ConstantMatrix A DelayedArray subclass that contains a constant value
ConstantMatrix-class A DelayedArray subclass that contains a constant value
contentIsPristine Simplify a tree of delayed operations
currentBlockId blockApply() and family
currentViewport blockApply() and family

-- D --

dbinom Statistical functions on DelayedArray objects
dbinom-method Statistical functions on DelayedArray objects
defaultAutoGrid Create automatic grids to use for block processing of array-like objects
defaultSinkAutoGrid Create automatic grids to use for block processing of array-like objects
DelayedAbind DelayedAbind objects
DelayedAbind-class DelayedAbind objects
DelayedAperm DelayedAperm objects
DelayedAperm-class DelayedAperm objects
DelayedArray DelayedArray objects
DelayedArray-class DelayedArray objects
DelayedArray-method A DelayedArray subclass that contains a constant value
DelayedArray-method DelayedArray objects
DelayedArray-method RleArray objects
DelayedArray-stats Statistical functions on DelayedArray objects
DelayedArray-utils Common operations on DelayedArray objects
DelayedArray1 DelayedArray objects
DelayedArray1-class DelayedArray objects
DelayedMatrix DelayedArray objects
DelayedMatrix-class DelayedArray objects
DelayedMatrix-stats DelayedMatrix row/col summarization
DelayedMatrix-utils Common operations on DelayedMatrix objects
DelayedNaryIsoOp DelayedNaryIsoOp objects
DelayedNaryIsoOp-class DelayedNaryIsoOp objects
DelayedNaryOp DelayedOp objects
DelayedNaryOp-class DelayedOp objects
DelayedOp DelayedOp objects
DelayedOp-class DelayedOp objects
DelayedSetDimnames DelayedSetDimnames objects
DelayedSetDimnames-class DelayedSetDimnames objects
DelayedSubassign DelayedSubassign objects
DelayedSubassign-class DelayedSubassign objects
DelayedSubset DelayedSubset objects
DelayedSubset-class DelayedSubset objects
DelayedUnaryIsoOp DelayedOp objects
DelayedUnaryIsoOp-class DelayedOp objects
DelayedUnaryIsoOpStack DelayedUnaryIsoOpStack objects
DelayedUnaryIsoOpStack-class DelayedUnaryIsoOpStack objects
DelayedUnaryIsoOpWithArgs DelayedUnaryIsoOpWithArgs objects
DelayedUnaryIsoOpWithArgs-class DelayedUnaryIsoOpWithArgs objects
DelayedUnaryOp DelayedOp objects
DelayedUnaryOp-class DelayedOp objects
dense2sparse SparseArraySeed objects
dim-method ArrayGrid and ArrayViewport objects
dim-method DelayedAbind objects
dim-method DelayedAperm objects
dim-method DelayedArray objects
dim-method DelayedNaryIsoOp objects
dim-method DelayedOp objects
dim-method DelayedSubset objects
dim-method RleArraySeed objects
dim-method Write blocks of data to a RealizationSink
dim<--method DelayedArray objects
dimnames-method DelayedAbind objects
dimnames-method DelayedAperm objects
dimnames-method DelayedArray objects
dimnames-method DelayedNaryIsoOp objects
dimnames-method DelayedOp objects
dimnames-method DelayedSetDimnames objects
dimnames-method DelayedSubset objects
dimnames-method RleArraySeed objects
dimnames-method SparseArraySeed objects
dimnames<--method DelayedArray objects
dimnames<--method SparseArraySeed objects
dims ArrayGrid and ArrayViewport objects
dims-method ArrayGrid and ArrayViewport objects
dlogis Statistical functions on DelayedArray objects
dlogis-method Statistical functions on DelayedArray objects
dnorm Statistical functions on DelayedArray objects
dnorm-method Statistical functions on DelayedArray objects
downsample ArrayGrid and ArrayViewport objects
downsample-method ArrayGrid and ArrayViewport objects
dpois Statistical functions on DelayedArray objects
dpois-method Statistical functions on DelayedArray objects
drop-method DelayedArray objects
DummyArrayGrid ArrayGrid and ArrayViewport objects
DummyArrayGrid-class ArrayGrid and ArrayViewport objects
DummyArrayViewport ArrayGrid and ArrayViewport objects
DummyArrayViewport-class ArrayGrid and ArrayViewport objects

-- E --

effectiveGrid blockApply() and family
end-method ArrayGrid and ArrayViewport objects
extract_array-method A DelayedArray subclass that contains a constant value
extract_array-method DelayedAbind objects
extract_array-method DelayedAperm objects
extract_array-method DelayedArray objects
extract_array-method DelayedNaryIsoOp objects
extract_array-method DelayedOp objects
extract_array-method DelayedSubassign objects
extract_array-method DelayedSubset objects
extract_array-method DelayedUnaryIsoOpStack objects
extract_array-method DelayedUnaryIsoOpWithArgs objects
extract_array-method RleArraySeed objects
extract_array-method SparseArraySeed objects
extract_sparse_array SparseArraySeed objects
extract_sparse_array-method A DelayedArray subclass that contains a constant value
extract_sparse_array-method DelayedAbind objects
extract_sparse_array-method DelayedAperm objects
extract_sparse_array-method DelayedNaryIsoOp objects
extract_sparse_array-method DelayedOp objects
extract_sparse_array-method DelayedSubassign objects
extract_sparse_array-method DelayedSubset objects
extract_sparse_array-method DelayedUnaryIsoOpStack objects
extract_sparse_array-method DelayedUnaryIsoOpWithArgs objects
extract_sparse_array-method SparseArraySeed objects

-- G --

getAutoBlockLength Control the geometry of automatic blocks
getAutoBlockShape Control the geometry of automatic blocks
getAutoBlockSize Control the geometry of automatic blocks
getAutoBPPARAM blockApply() and family
getAutoGridMaker Create automatic grids to use for block processing of array-like objects
getAutoRealizationBackend Write blocks of data to a RealizationSink
getRealizationBackend Write blocks of data to a RealizationSink
get_type_size Control the geometry of automatic blocks
grepl-method Common operations on DelayedArray objects
gridApply blockApply() and family
gridReduce blockApply() and family
gsub-method Common operations on DelayedArray objects

-- I --

is.finite-method Common operations on DelayedArray objects
is.infinite-method Common operations on DelayedArray objects
is.infinite-method Operate natively on SparseArraySeed objects
is.na-method Common operations on DelayedArray objects
is.na-method Operate natively on SparseArraySeed objects
is.nan-method Common operations on DelayedArray objects
is.nan-method Operate natively on SparseArraySeed objects
isLinear Utilities to make capped volume boxes
isLinear-method Utilities to make capped volume boxes
isPristine Simplify a tree of delayed operations
is_noop DelayedOp objects
is_noop-method DelayedAbind objects
is_noop-method DelayedAperm objects
is_noop-method DelayedSetDimnames objects
is_noop-method DelayedSubassign objects
is_noop-method DelayedSubset objects
is_sparse Read array blocks
is_sparse-method A DelayedArray subclass that contains a constant value
is_sparse-method DelayedAbind objects
is_sparse-method DelayedAperm objects
is_sparse-method DelayedNaryIsoOp objects
is_sparse-method DelayedOp objects
is_sparse-method DelayedSubassign objects
is_sparse-method DelayedSubset objects
is_sparse-method DelayedUnaryIsoOpStack objects
is_sparse-method DelayedUnaryIsoOpWithArgs objects
is_sparse-method SparseArraySeed objects
is_sparse<- SparseArraySeed objects

-- L --

L-index Manipulation of array selections
lengths-method ArrayGrid and ArrayViewport objects
lengths-method Common operations on DelayedArray objects
Lindex Manipulation of array selections
Lindex2Mindex Manipulation of array selections
linearInd Manipulation of array selections
log-method Common operations on DelayedArray objects

-- M --

M-index Manipulation of array selections
makeCappedVolumeBox Utilities to make capped volume boxes
makeNindexFromArrayViewport ArrayGrid and ArrayViewport objects
makeRegularArrayGridOfCappedLengthViewports Utilities to make capped volume boxes
matrixClass DelayedArray objects
matrixClass-method A DelayedArray subclass that contains a constant value
matrixClass-method DelayedArray objects
matrixClass-method RleArray objects
max-method Operate natively on SparseArraySeed objects
maxlength ArrayGrid and ArrayViewport objects
maxlength-method ArrayGrid and ArrayViewport objects
mean Common operations on DelayedArray objects
mean-method Common operations on DelayedArray objects
mean-method Operate natively on SparseArraySeed objects
mean.DelayedArray Common operations on DelayedArray objects
mean.SparseArraySeed Operate natively on SparseArraySeed objects
min-method Operate natively on SparseArraySeed objects
Mindex Manipulation of array selections
Mindex2Lindex Manipulation of array selections
modify_seeds Visualize and access the leaves of a tree of delayed operations

-- N --

N-index Manipulation of array selections
names-method DelayedArray objects
names<--method DelayedArray objects
nchar-method Common operations on DelayedArray objects
nchar-method Operate natively on SparseArraySeed objects
netSubsetAndAperm Simplify a tree of delayed operations
netSubsetAndAperm-method Simplify a tree of delayed operations
new_DelayedArray DelayedArray objects
Nindex Manipulation of array selections
nseed Visualize and access the leaves of a tree of delayed operations
nseed-method Visualize and access the leaves of a tree of delayed operations
nzdata SparseArraySeed objects
nzdata-method SparseArraySeed objects
nzindex SparseArraySeed objects
nzindex-method SparseArraySeed objects

-- P --

path Visualize and access the leaves of a tree of delayed operations
path-method Visualize and access the leaves of a tree of delayed operations
path<--method Visualize and access the leaves of a tree of delayed operations
pbinom Statistical functions on DelayedArray objects
pbinom-method Statistical functions on DelayedArray objects
plogis Statistical functions on DelayedArray objects
plogis-method Statistical functions on DelayedArray objects
pmax2 Common operations on DelayedArray objects
pmax2-method Common operations on DelayedArray objects
pmin2 Common operations on DelayedArray objects
pmin2-method Common operations on DelayedArray objects
pnorm Statistical functions on DelayedArray objects
pnorm-method Statistical functions on DelayedArray objects
ppois Statistical functions on DelayedArray objects
ppois-method Statistical functions on DelayedArray objects
prod-method Operate natively on SparseArraySeed objects

-- Q --

qbinom Statistical functions on DelayedArray objects
qbinom-method Statistical functions on DelayedArray objects
qlogis Statistical functions on DelayedArray objects
qlogis-method Statistical functions on DelayedArray objects
qnorm Statistical functions on DelayedArray objects
qnorm-method Statistical functions on DelayedArray objects
qpois Statistical functions on DelayedArray objects
qpois-method Statistical functions on DelayedArray objects

-- R --

range Common operations on DelayedArray objects
range-method Common operations on DelayedArray objects
range-method Operate natively on SparseArraySeed objects
range.DelayedArray Common operations on DelayedArray objects
range.SparseArraySeed Operate natively on SparseArraySeed objects
ranges-method ArrayGrid and ArrayViewport objects
rbind Common operations on DelayedArray objects
rbind-method Common operations on DelayedArray objects
rbind-method Operate natively on SparseArraySeed objects
read_block Read array blocks
read_block-method Read array blocks
read_sparse_block Read array blocks
read_sparse_block-method Read array blocks
RealizationSink Write blocks of data to a RealizationSink
RealizationSink-class Write blocks of data to a RealizationSink
realize Realize a DelayedArray object
realize-method Realize a DelayedArray object
refdim ArrayGrid and ArrayViewport objects
refdim-method ArrayGrid and ArrayViewport objects
RegularArrayGrid ArrayGrid and ArrayViewport objects
RegularArrayGrid-class ArrayGrid and ArrayViewport objects
RleArray RleArray objects
RleArray-class RleArray objects
RleArraySeed RleArraySeed objects
RleArraySeed-class RleArraySeed objects
RleMatrix RleArray objects
RleMatrix-class RleArray objects
RleRealizationSink RleArraySeed objects
RleRealizationSink-class RleArraySeed objects
round-method Common operations on DelayedArray objects
rowAutoGrid Create automatic grids to use for block processing of array-like objects
rowGrid Create automatic grids to use for block processing of array-like objects
rowMaxs DelayedMatrix row/col summarization
rowMaxs-method DelayedMatrix row/col summarization
rowMeans DelayedMatrix row/col summarization
rowMeans-method DelayedMatrix row/col summarization
rowMins DelayedMatrix row/col summarization
rowMins-method DelayedMatrix row/col summarization
rowRanges DelayedMatrix row/col summarization
rowRanges-method DelayedMatrix row/col summarization
rowsum Common operations on DelayedMatrix objects
rowsum-method Common operations on DelayedMatrix objects
rowsum-method sparseMatrix utilities
rowsum.DelayedMatrix Common operations on DelayedMatrix objects
rowsum.dgCMatrix sparseMatrix utilities
rowSums DelayedMatrix row/col summarization
rowSums-method DelayedMatrix row/col summarization

-- S --

SafeArrayViewport ArrayGrid and ArrayViewport objects
SafeArrayViewport-class ArrayGrid and ArrayViewport objects
scale Common operations on DelayedArray objects
scale-method Common operations on DelayedArray objects
scale.DelayedMatrix Common operations on DelayedArray objects
seed Visualize and access the leaves of a tree of delayed operations
seed-method Visualize and access the leaves of a tree of delayed operations
seed<- Visualize and access the leaves of a tree of delayed operations
seed<--method Visualize and access the leaves of a tree of delayed operations
seedApply Visualize and access the leaves of a tree of delayed operations
setAutoBlockShape Control the geometry of automatic blocks
setAutoBlockSize Control the geometry of automatic blocks
setAutoBPPARAM blockApply() and family
setAutoGridMaker Create automatic grids to use for block processing of array-like objects
setAutoRealizationBackend Write blocks of data to a RealizationSink
setRealizationBackend Write blocks of data to a RealizationSink
set_grid_context blockApply() and family
show-method ArrayGrid and ArrayViewport objects
show-method DelayedArray objects
show-method Visualize and access the leaves of a tree of delayed operations
showtree Visualize and access the leaves of a tree of delayed operations
signif-method Common operations on DelayedArray objects
simplify Simplify a tree of delayed operations
simplify-method Simplify a tree of delayed operations
sinkApply Write blocks of data to a RealizationSink
SolidRleArraySeed RleArraySeed objects
SolidRleArraySeed-class RleArraySeed objects
sparse2dense SparseArraySeed objects
SparseArraySeed SparseArraySeed objects
SparseArraySeed-class SparseArraySeed objects
SparseArraySeed-utils Operate natively on SparseArraySeed objects
sparseMatrix-utils sparseMatrix utilities
sparsity SparseArraySeed objects
sparsity-method SparseArraySeed objects
split-method DelayedArray objects
split.DelayedArray DelayedArray objects
splitAsList-method DelayedArray objects
start-method ArrayGrid and ArrayViewport objects
sub-method Common operations on DelayedArray objects
sum-method Operate natively on SparseArraySeed objects
summary-method DelayedAbind objects
summary-method DelayedAperm objects
summary-method DelayedNaryIsoOp objects
summary-method DelayedOp objects
summary-method DelayedSetDimnames objects
summary-method DelayedSubassign objects
summary-method DelayedSubset objects
summary-method DelayedUnaryIsoOpStack objects
summary-method DelayedUnaryIsoOpWithArgs objects
summary.DelayedAbind DelayedAbind objects
summary.DelayedAperm DelayedAperm objects
summary.DelayedNaryIsoOp DelayedNaryIsoOp objects
summary.DelayedOp DelayedOp objects
summary.DelayedSetDimnames DelayedSetDimnames objects
summary.DelayedSubassign DelayedSubassign objects
summary.DelayedSubset DelayedSubset objects
summary.DelayedUnaryIsoOpStack DelayedUnaryIsoOpStack objects
summary.DelayedUnaryIsoOpWithArgs DelayedUnaryIsoOpWithArgs objects
supportedRealizationBackends Write blocks of data to a RealizationSink
sweep Common operations on DelayedArray objects
sweep-method Common operations on DelayedArray objects

-- T --

t Common operations on DelayedMatrix objects
table Common operations on DelayedArray objects
table-method Common operations on DelayedArray objects
tolower-method Common operations on DelayedArray objects
tolower-method Operate natively on SparseArraySeed objects
toupper-method Common operations on DelayedArray objects
toupper-method Operate natively on SparseArraySeed objects
type DelayedArray objects
type-method RleArraySeed objects
type<--method Common operations on DelayedArray objects

-- U --

unique Common operations on DelayedArray objects
unique-method Common operations on DelayedArray objects
unique.DelayedArray Common operations on DelayedArray objects
updateObject-method DelayedAbind objects
updateObject-method DelayedAperm objects
updateObject-method DelayedArray objects
updateObject-method DelayedNaryIsoOp objects
updateObject-method DelayedOp objects
updateObject-method DelayedSetDimnames objects

-- V --

viewportApply blockApply() and family
viewportReduce blockApply() and family

-- W --

which-method Common operations on DelayedArray objects
which-method Operate natively on SparseArraySeed objects
width-method ArrayGrid and ArrayViewport objects
write_block Write blocks of data to a RealizationSink
write_block-method RleArray objects
write_block-method Write blocks of data to a RealizationSink

-- misc --

!-method Common operations on DelayedArray objects
%*% Common operations on DelayedMatrix objects
%*%-method Common operations on DelayedMatrix objects
+-method Common operations on DelayedArray objects
--method Common operations on DelayedArray objects
[-method DelayedArray objects
[<--method DelayedArray objects
[[-method DelayedArray objects