Added scripts to generate the PBMC datasets.

10x-pbmc/README.md

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+# 10X Genomics PBMC single-cell RNA-seq dataset
+
+This uses some of the older 10X Genomics test datasets, namely the 3K and 4K PBMC datasets.
+These should be some kind of replicatese but I have long forgotten what they are - 
+I got them from the [**TENxPBMCData**](https://bioconductor.org/packages/TENxPBMCData) package, so go figure.
+Run `generate.R` to construct the files.

10x-pbmc/generate.R

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+library(TENxPBMCData)
+sce3 <- TENxPBMCData("pbmc3k")
+colnames(sce3) <- sce3$Barcode
+assay(sce3) <- as(assay(sce3), "dgCMatrix")
+
+sce4 <- TENxPBMCData("pbmc4k")
+colnames(sce4) <- sce4$Barcode
+assay(sce4) <- as(assay(sce4), "dgCMatrix")
+
+# Saving in version 3 of the 10x format.
+library(DropletUtils)
+write10xCounts("mtx-pbmc3k", assay(sce3), gene.symbol=rowData(sce3)$Symbol, version="3", overwrite=TRUE)
+write10xCounts("mtx-pbmc4k", assay(sce4), gene.symbol=rowData(sce4)$Symbol, version="3", overwrite=TRUE)
+
+# Saving in version 3 of the 10x format.
+source("../_scripts/compact10x.R")
+
+name <- "pbmc3k-tenx.h5"
+unlink(name)
+compact10x(name, assay(sce3), rownames(sce3), rowData(sce3)$Symbol)
+
+name <- "pbmc4k-tenx.h5"
+unlink(name)
+compact10x(name, assay(sce4), rownames(sce4), rowData(sce4)$Symbol)
+
+# Combining into a single object.
+common <- intersect(rownames(sce3), rownames(sce4))
+x <- cbind(
+    assay(sce3)[common,,drop=FALSE],
+    assay(sce4)[common,,drop=FALSE]
+)
+write10xCounts("combined", x, 
+    gene.symbol=rowData(sce3)[match(common, rownames(sce3)),"Symbol"],
+    version="3", overwrite=TRUE)
+
+Y <- read.delim('combined/barcodes.tsv.gz', header=FALSE)
+Y$V2 <- rep(c("3k", "4k"), c(ncol(sce3), ncol(sce4)))
+gzhandle <- gzfile("combined/barcodes.tsv.gz", open="wb")
+write.table(gzhandle, x=Y, sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)
+close(gzhandle)