noCorrect {batchelor} | 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, assay.type = "logcounts")
... |
One or more log-expression matrices where genes correspond to rows and cells correspond to columns, if 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.
Objects of different types can be mixed together.
If a single object is supplied, |
batch |
A 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 retain. |
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.
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)