noCorrect {batchelor}R Documentation

No correction

Description

Provides a no-correction method that has the same interface as the correction functions. This allows users to easily swap function calls to examine the effect of correction.

Usage

noCorrect(..., batch = NULL, subset.row = NULL, assay.type = "logcounts")

Arguments

...

One or more log-expression matrices where genes correspond to rows and cells correspond to columns, if pc.input=FALSE. Each matrix should contain the same number of rows, corresponding to the same genes in the same order.

Alternatively, one or more SingleCellExperiment objects can be supplied containing a log-expression matrix in the assay.type assay. Note the same restrictions described above for gene expression matrix inputs.

If multiple objects are supplied, each object is assumed to contain all and only cells from a single batch. Objects of different types can be mixed together. If a single object is supplied, batch should also be specified.

batch

A factor specifying the batch of origin for all cells when only a single object is supplied in .... This is ignored if multiple objects are present.

subset.row

A vector specifying which features to retain.

assay.type

A string or integer scalar specifying the assay containing the log-expression values. Only used for SingleCellExperiment inputs.

Details

This function is effectively equivalent to cbinding the matrices together without any correction. The aim is to provide a consistent interface that allows users to simply combine batches without additional operations. This is often desirable as a negative control to see if the transformation is actually beneficial. It also allows for convenient downstream analyses that are based on the uncorrected data, e.g., differential expression.

Value

A SingleCellExperiment is returned where each row is a gene and each column is a cell. This contains:

Author(s)

Aaron Lun

Examples

B1 <- matrix(rnorm(10000), ncol=50) # Batch 1 
B2 <- matrix(rnorm(10000), ncol=50) # Batch 2
out <- noCorrect(B1, B2)

# Same as combining the expression values.
stopifnot(all(assay(out)==cbind(B1, B2)))

# Specifies which cell came from which batch:
str(out$batch)

[Package batchelor version 1.2.4 Index]