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 `cbind`ing 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:

- A `merged` matrix in the `assays` slot, containing the merged expression values from all elements of `...`.

- A `batch` column in the `colData` slot, containing the batch of origin for each row (i.e., cell) in `corrected`.

### 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]