Description Details See Also Examples
Common operations on DelayedArray objects.
The operations currently supported on DelayedArray objects are:
Delayed operations:
rbind
and cbind
all the members of the Ops
,
Math
, and Math2
groups
sweep
!
is.na
, is.finite
, is.infinite
, is.nan
type<-
lengths
nchar
, tolower
, toupper
,
grepl
, sub
, gsub
pmax2
and pmin2
statistical functions like dnorm
, dbinom
, dpois
,
and dlogis
(for the Normal, Binomial, Poisson, and Logistic
distribution, respectively) and related functions (documented in
DelayedArray-stats)
Block-processed operations:
anyNA
, which
unique
, table
all the members of the Summary
group
mean
apply
cbind
in the base package for
rbind/cbind'ing ordinary arrays.
arbind
and acbind
in this package
(DelayedArray) for binding ordinary arrays of arbitrary
dimensions along their rows or columns.
is.na
, !
,
table
, mean
,
apply
, and %*%
in the
base package for the corresponding operations on ordinary
arrays or matrices.
DelayedMatrix-utils for common operations on DelayedMatrix objects.
DelayedArray-stats for statistical functions on DelayedArray objects.
DelayedMatrix-stats for DelayedMatrix row/col summarization.
DelayedArray objects.
HDF5Array objects in the HDF5Array package.
S4groupGeneric
in the methods package
for the members of the Ops
,
Math
, and Math2
groups.
array objects in base R.
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## BIND DelayedArray OBJECTS
## ---------------------------------------------------------------------
## DelayedArray objects can be bound along their 1st (rows) or 2nd
## (columns) dimension with rbind() or cbind(). These operations are
## equivalent to arbind() and acbind(), respectively, and are all
## delayed.
## On 2D objects:
library(HDF5Array)
toy_h5 <- system.file("extdata", "toy.h5", package="HDF5Array")
h5ls(toy_h5)
M1 <- HDF5Array(toy_h5, "M1")
M2 <- HDF5Array(toy_h5, "M2")
M12 <- rbind(M1, t(M2)) # delayed
M12
colMeans(M12) # block-processed
## On objects with more than 2 dimensions:
example(arbind) # to create arrays a1, a2, a3
A1 <- DelayedArray(a1)
A2 <- DelayedArray(a2)
A3 <- DelayedArray(a3)
A123 <- rbind(A1, A2, A3) # delayed
A123
## On 1D objects:
v1 <- array(11:15, 5, dimnames=list(LETTERS[1:5]))
v2 <- array(letters[1:3])
V1 <- DelayedArray(v1)
V2 <- DelayedArray(v2)
V12 <- rbind(V1, V2)
V12
## Not run: cbind(V1, V2) # Error! (the objects to cbind() must have at least 2
# dimensions)
## End(Not run)
## Note that base::rbind() and base::cbind() do something completely
## different on ordinary arrays that are not matrices. They treat them
## as if they were vectors:
rbind(a1, a2, a3)
cbind(a1, a2, a3)
rbind(v1, v2)
cbind(v1, v2)
## Also note that DelayedArray objects of arbitrary dimensions can be
## stored inside a DataFrame object as long as they all have the same
## first dimension (nrow()):
DF <- DataFrame(M=I(tail(M1, n=5)), A=I(A3), V=I(V1))
DF[-3, ]
DF2 <- rbind(DF, DF)
DF2$V
## Sanity checks:
m1 <- as.matrix(M1)
m2 <- as.matrix(M2)
stopifnot(identical(rbind(m1, t(m2)), as.matrix(M12)))
stopifnot(identical(arbind(a1, a2, a3), as.array(A123)))
stopifnot(identical(arbind(v1, v2), as.array(V12)))
stopifnot(identical(rbind(DF$M, DF$M), DF2$M))
stopifnot(identical(rbind(DF$A, DF$A), DF2$A))
stopifnot(identical(rbind(DF$V, DF$V), DF2$V))
## ---------------------------------------------------------------------
## MORE OPERATIONS
## ---------------------------------------------------------------------
M1 >= 0.5 & M1 < 0.75 # delayed
log(M1) # delayed
pmax2(M2, 0) # delayed
type(M2) <- "integer" # delayed
M2
## table() is block-processed:
a4 <- array(sample(50L, 2000000L, replace=TRUE), c(200, 4, 2500))
A4 <- as(a4, "HDF5Array")
table(A4)
a5 <- array(sample(20L, 2000000L, replace=TRUE), c(200, 4, 2500))
A5 <- as(a5, "HDF5Array")
table(A5)
A4 - 2 * A5 # delayed
table(A4 - 2 * A5) # block-processed
## range() is block-processed:
range(A4 - 2 * A5)
range(M1)
cmeans <- colMeans(M2) # block-processed
sweep(M2, 2, cmeans) # delayed
|
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