The TENxMatrix container is now implemented in the HDF5Array package

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: TENxGenomics
 Title: Interface to 10x Genomics data
-Version: 0.0.27
+Version: 0.0.28
 Authors@R:
     c(person(
         "Martin", "Morgan", email = "[email protected]",
@@ -21,13 +21,12 @@ Description: This package provides an interface to 10xGenomics data,
 Depends: R (>= 3.4.0), methods, Matrix, SummarizedExperiment,
     DelayedArray (>= 0.3.7)
 Imports: rhdf5 (>= 2.19.3-2), tools, BiocGenerics, S4Vectors, IRanges,
-    HDF5Array (>= 1.7.6), BiocParallel (>= 1.11.2)
+    HDF5Array (>= 1.9.6), BiocParallel (>= 1.11.2)
 Suggests: BiocStyle, knitr, rmarkdown, BiocFileCache,
     Rtsne, BiocSklearn, restfulSE
 Collate:
     TENxGenomics-class.R
     coerce.R
-    TENxMatrix-class.R
     tenxSummarizedExperiment.R
     tenxiterate.R
 License: Artistic-2.0

NAMESPACE

@@ -2,7 +2,6 @@
 
 S3method(as.matrix,TENxGenomics)
 export(TENxGenomics)
-export(TENxMatrix)
 export(as.dgCMatrix)
 export(as.dgCMatrixSummarizedExperiment)
 export(as.matrixSummarizedExperiment)
@@ -11,8 +10,6 @@ export(dgCMatrixSummarizedExperiment)
 export(matrixSummarizedExperiment)
 export(tenxSummarizedExperiment)
 export(tenxiterate)
-exportClasses(TENxMatrix)
-exportClasses(TENxMatrixSeed)
 exportMethods("[")
 exportMethods(coerce)
 exportMethods(dim)

vignettes/TENxGenomics.Rmd

@@ -20,6 +20,7 @@ knitr::opts_chunk$set(
 suppressPackageStartupMessages({
     library(TENxGenomics)
     library(BiocFileCache)
+    library(HDF5Array)
     library(SummarizedExperiment)
     library(Rtsne)
 })
@@ -104,16 +105,18 @@ as.matrix(tenx[sample(nrow(tenx), 5), sample(ncol(tenx), 3)])
 ## Using a TENxMatrix object
 
 An alternative to creating `TENxGenomics` object `tenx` is to wrap the
-10xGenomics data in a `TENxMatrix` object.
+10xGenomics data in a `TENxMatrix` object. The `TENxMatrix` container is
+implemented in the [HDF5Array][] package.
 
 ```{r}
+library(HDF5Array)
 tenxmat <- TENxMatrix(path)
 ```
 
 The `TENxMatrix` class extends the `DelayedArray` class defined in the
 [DelayedArray][] package so all the operations available on `DelayedArray`
-objects work on `TENxMatrix` objects. See `?DelayedArray` for more
-information.
+objects work on `TENxMatrix` objects. See `?TENxMatrix` and `?DelayedArray`
+for more information.
 
 ## Rich
 
@@ -304,3 +307,4 @@ sessionInfo()
 [BiocFileCache]: https://bioconductor.org/packages/BiocFileCache
 [SummarizedExperiment]: https://bioconductor.org/packages/SummarizedExperiment
 [DelayedArray]: https://bioconductor.org/packages/DelayedArray
+[HDF5Array]: https://bioconductor.org/packages/HDF5Array