noCorrect | R Documentation |

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.

```
noCorrect(
...,
batch = NULL,
subset.row = NULL,
correct.all = FALSE,
assay.type = "logcounts"
)
```

`...` |
One or more log-expression matrices where genes correspond to rows and cells correspond to columns.
Alternatively, one or more SingleCellExperiment objects can be supplied containing a log-expression matrix in the If multiple objects are supplied, each object is assumed to contain all and only cells from a single batch.
If a single object is supplied, it is assumed to contain cells from all batches, so Alternatively, one or more lists of matrices or SingleCellExperiments can be provided;
this is flattened as if the objects inside each list were passed directly to |

`batch` |
A vector or factor specifying the batch of origin for all cells when only a single object is supplied in |

`subset.row` |
A vector specifying which features to use for correction. |

`correct.all` |
Logical scalar indicating whether corrected expression values should be computed for genes not in |

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

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.

Setting `correct.all=TRUE`

is equivalent to forcing `subset.row=NULL`

,
given that no correction is being performed anyway.

In the case of a single object in `...`

,
`batch`

has no effect beyond being stored in the `colData`

of the output.

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`

.

Aaron Lun

```
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)
```

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.