inst/doc/userguide.R

In TileDBArray: Using TileDB as a DelayedArray Backend

## ---- echo=FALSE, results="hide"----------------------------------------------
knitr::opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE)
library(BiocStyle)

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X <- matrix(rnorm(1000), ncol=10)
library(TileDBArray)
writeTileDBArray(X)

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as(X, "TileDBArray")

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Y <- Matrix::rsparsematrix(1000, 1000, density=0.01)
writeTileDBArray(Y)

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writeTileDBArray(Y > 0)

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rownames(X) <- sprintf("GENE_%i", seq_len(nrow(X)))
colnames(X) <- sprintf("SAMP_%i", seq_len(ncol(X)))
writeTileDBArray(X)

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out <- as(X, "TileDBArray")
dim(out)
head(rownames(out))
head(out[,1])

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out[1:5,1:5] 
out * 2

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colSums(out)
out %*% runif(ncol(out))

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X <- matrix(rnorm(1000), ncol=10)
path <- tempfile()
writeTileDBArray(X, path=path, attr="WHEE")

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path2 <- tempfile()
setTileDBPath(path2)
as(X, "TileDBArray") # uses path2 to store the backend.

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sessionInfo()