suppressPackageStartupMessages(library(TENxPBMCData))
require(scry)

## Loading required package: scry

We illustrate the application of scry methods to disk-based data from the TENxPBMCData package. Each dataset in this package is stored in an HDF5 file that is accessed through a DelayedArray interface. This avoids the need to load the entire dataset into memory for analysis.

Feature Selection with Deviance

sce<-TENxPBMCData(dataset="pbmc3k")

## snapshotDate(): 2022-04-19

## see ?TENxPBMCData and browseVignettes('TENxPBMCData') for documentation

## loading from cache

h5counts<-counts(sce)
seed(h5counts) #print information about object

## An object of class "HDF5ArraySeed"
## Slot "filepath":
## [1] "/var/cache/biocbuild_cache/R/ExperimentHub/80cdc310cb06_1605"
## 
## Slot "name":
## [1] "/counts"
## 
## Slot "as_sparse":
## [1] TRUE
## 
## Slot "type":
## [1] NA
## 
## Slot "dim":
## [1] 32738  2700
## 
## Slot "chunkdim":
## [1] 631  52
## 
## Slot "first_val":
## [1] 0

h5counts<-h5counts[rowSums(h5counts)>0,]
system.time(h5devs<-devianceFeatureSelection(h5counts)) # 26 sec

##    user  system elapsed 
##  32.583   4.507  37.091

We now compare the computation speed when the same data is converted to an ordinary array in-memory. Note this would not be possible with larger HDF5Array objects.

denseCounts<-as.matrix(h5counts)
system.time(denseDevs<-devianceFeatureSelection(denseCounts)) # 5 sec

##    user  system elapsed 
##   5.695   0.999   6.696

max(abs(denseDevs-h5devs)) #should be close to zero

## [1] 0

Finally we compare the speed when the counts data are stored in a sparse in-memory Matrix format

mean(denseCounts>0) #shows that the data are mostly zeros so sparsity useful

## [1] 0.05091945

sparseCounts<-Matrix::Matrix(denseCounts,sparse=TRUE)
system.time(sparseDevs<-devianceFeatureSelection(sparseCounts)) #1.6 sec

##    user  system elapsed 
##   1.126   0.495   1.621

max(abs(sparseDevs-h5devs)) #should be close to zero

## [1] 1.629815e-09

Using disk-based data saves memory but slows computation time. When the data contain mostly zeros, and are not too large, the sparse in-memory Matrix object achieves fastest computation times. The resulting deviance statistics are the same for all of the different data formats.

Null residuals

One can run nullResiduals on HDF5Matrix, DelayedArray matrices, and sparse matrices from the Matrix package with the same syntax used for the base matrix case.

We illustrate this with the same dataset from the TENxPBMCData package.

sce <- nullResiduals(sce, assay="counts", type="deviance")
str(sce)