runSCMerge: Apply scMerge batch effect correction method to...

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Apply scMerge batch effect correction method to SingleCellExperiment object

Description

The scMerge method leverages factor analysis, stably expressed genes (SEGs) and (pseudo-) replicates to remove unwanted variations and merge multiple scRNA-Seq data.

Usage

runSCMerge(
  inSCE,
  useAssay = "logcounts",
  batch = "batch",
  assayName = "scMerge",
  hvgExprs = "counts",
  seg = NULL,
  kmeansK = NULL,
  cellType = NULL,
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

inSCE	Input SingleCellExperiment object
useAssay	A single character indicating the name of the assay requiring batch correction. Default "logcounts".
batch	A single character indicating a field in colData that annotates the batches. Default "batch".
assayName	A single characeter. The name for the corrected assay. Will be saved to assay. Default "scMerge".
hvgExprs	A single characeter. The assay that to be used for highly variable genes identification. Default "counts".
seg	A vector of gene names or indices that specifies SEG (Stably Expressed Genes) set as negative control. Pre-defined dataset with human and mouse SEG lists is available with segList or segList_ensemblGeneID. Default NULL, and this value will be auto-detected by default with scSEGIndex.
kmeansK	An integer vector. Indicating the kmeans' K-value for each batch (i.e. how many subclusters in each batch should exist), in order to construct pseudo-replicates. The length of codekmeansK needs to be the same as the number of batches. Default NULL, and this value will be auto-detected by default, depending on cellType.
cellType	A single character. A string indicating a field in colData(inSCE) that defines different cell types. Default 'cell_type'.
BPPARAM	A BiocParallelParam object specifying whether should be parallelized. Default BiocParallel::SerialParam().

Value

The input SingleCellExperiment object with assay(inSCE, assayName) updated.

References

Hoa, et al., 2020

Examples

data('sceBatches', package = 'singleCellTK')
## Not run: 
logcounts(sceBatches) <- log1p(counts(sceBatches))
sceCorr <- runSCMerge(sceBatches)

## End(Not run)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.