downsampleCounts {scater} | R Documentation

## Downsample a count matrix

### Description

Downsample a count matrix to a desired proportion.

### Usage

    downsampleCounts(x, prop)

### Arguments

`x` | matrix of counts
`prop` | numeric scalar or vector of length `ncol(x)` in [0, 1] indicating the downsampling proportion

### Details

Given multiple 10X batches of very different sequencing depths, it can be beneficial to downsample the deepest batches to match the coverage of the shallowest batches. This avoids differences in technical noise that can drive clustering by batch.

Downsampling without replacement is performed on the counts in each cell to generate the output matrix. Each count in the returned matrix is guaranteed to be smaller than the original value in `x`. This provides an alternative to downsampling in the CellRanger `aggr` function.

### Value

an integer matrix of downsampled counts

### Examples

    sce10x <- read10xResults(system.file("extdata", package="scater"))
    downsampled <- downsampleCounts(counts(sce10x), prop = 0.5)

[Package scater version 1.6.3 Index]