divideIntoBatches: Divide into batches

In LTLA/batchelor: Single-Cell Batch Correction Methods

Divide into batches

Description

Divide a single input object into multiple separate objects according to their batch of origin.

Usage

divideIntoBatches(x, batch, byrow = FALSE, restrict = NULL)

Arguments

x	A matrix-like object where one dimension corresponds to cells and another represents features.
batch	A factor specifying the batch to which each cell belongs.
byrow	A logical scalar indicating whether rows correspond to cells.
restrict	A subsetting vector specifying which cells should be used for correction.

Details

This function is intended for internal use and other package developers. It splits a single input object into multiple batches, allowing developers to use the same code for the scenario where batch is supplied with a single input.

Value

A list containing:

• batches, a named list of matrix-like objects where each element corresponds to a level of batch and contains all cells from that batch.

• reorder, an integer vector to be applied to the combined batches to recover the ordering of cells in x.

• restricted, a named list of integer vectors specifying which cells are to be used for correction. Set to NULL if the input restrict was also NULL.

Author(s)

Aaron Lun

Examples

X <- matrix(rnorm(1000), ncol=100)
out <- divideIntoBatches(X, sample(3, 100, replace=TRUE))
names(out)

# Recovering original order.
Y <- do.call(cbind, out$batches)
Z <- Y[,out$reorder]
all.equal(Z, X) # should be TRUE.

LTLA/batchelor documentation built on Jan. 19, 2024, 6:33 p.m.