# Scry Methods For Larger Datasets

## Will Townes

### 04 June, 2025

    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")

    ## 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] "F:/biocbuild/ExperimentHub_cache/619459f042db_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
    ##   39.48    3.95   43.44

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
    ##    8.16    1.02    9.17

    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
    ##    1.91    0.48    2.40

    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)