scMerge2: Perform the scMerge2 algorithm
In SydneyBioX/scMerge: scMerge: Merging multiple batches of scRNA-seq data

scMerge2

R Documentation

Perform the scMerge2 algorithm

Description

Merge single-cell data from different batches and experiments leveraging (pseudo)-replicates, control genes and pseudo-bulk.

Usage

scMerge2(
  exprsMat,
  batch,
  cellTypes = NULL,
  condition = NULL,
  ctl = rownames(exprsMat),
  chosen.hvg = NULL,
  ruvK = 20,
  use_bpparam = BiocParallel::SerialParam(),
  use_bsparam = BiocSingular::RandomParam(),
  use_bnparam = BiocNeighbors::AnnoyParam(),
  pseudoBulk_fn = "create_pseudoBulk",
  k_pseudoBulk = 30,
  k_celltype = 10,
  exprsMat_counts = NULL,
  cosineNorm = TRUE,
  return_subset = FALSE,
  return_subset_genes = NULL,
  return_matrix = TRUE,
  byChunk = TRUE,
  chunkSize = 50000,
  verbose = TRUE,
  seed = 1
)

Arguments

`exprsMat`	A gene (row) by cell (column) log-transformed matrix to be adjusted.
`batch`	A vector indicating the batch information for each cell in the batch-combined matrix.
`cellTypes`	An optional vector indicating the cell type information for each cell in the batch-combined matrix. If it is `NULL`, pseudo-replicate procedure will be run to identify cell type.
`condition`	An optional vector indicating the condition information for each cell in the batch-combined matrix.
`ctl`	A character vector of negative control. It should have a non-empty intersection with the rows of exprsMat
`chosen.hvg`	An optional character vector of highly variable genes chosen.
`ruvK`	An integer indicates the number of unwanted variation factors that are removed, default is 20.
`use_bpparam`	A `BiocParallelParam` class object from the `BiocParallel` package is used. Default is SerialParam().
`use_bsparam`	A `BiocSingularParam` class object from the `BiocSingular` package is used. Default is RandomParam().
`use_bnparam`	A `BiocNeighborsParam` class object from the `BiocNeighbors` package is used. Default is AnnoyParam().
`pseudoBulk_fn`	A character indicates the way of pseudobulk constructed.
`k_pseudoBulk`	An integer indicates the number of pseudobulk constructed within each cell grouping. Default is 30.
`k_celltype`	An integer indicates the number of nearest neighbours used in `buildSNNGraph` when grouping cells within each batch. Default is 10.
`exprsMat_counts`	A gene (row) by cell (column) counts matrix to be adjusted.
`cosineNorm`	A logical vector indicates whether cosine normalisation is performed on input data.
`return_subset`	If `TRUE`, adjusted matrix of only a subset of genes (hvg or indicates in `return_subset_genes`) will be return.
`return_subset_genes`	An optional character vector of indicates the subset of genes will be adjusted.
`return_matrix`	A logical value indicates whether the adjusted matrix is calculated and returned.
`byChunk`	A logical value indicates whether it calculates the adjusted matrix by chunk
`chunkSize`	A numeric indicates the size of the chunk. If `FALSE`, then only the estimated parameters will be returned.
`verbose`	If `TRUE`, then all intermediate steps will be shown. Default to `FALSE`.
`seed`	A numeric input indicates the seed used.

Value

Returns a list object with following components:

newY: if return_matrix is TRUE, the adjusted matrix will be return.
fullalpha: Alpha estimated from the fastRUVIII model.
M: Replicate matrix.

Author(s)

Yingxin Lin

Examples

## Loading example data
data('example_sce', package = 'scMerge')
## Previously computed stably expressed genes
data('segList_ensemblGeneID', package = 'scMerge')
## Running an example data with minimal inputs
library(SingleCellExperiment)
exprsMat <- scMerge2(exprsMat = logcounts(example_sce),
batch = example_sce$batch,
ctl = segList_ensemblGeneID$mouse$mouse_scSEG)
assay(example_sce, "scMerge2") <- exprsMat$newY


example_sce = scater::runPCA(example_sce, exprs_values = 'scMerge2')                                       
scater::plotPCA(example_sce, colour_by = 'cellTypes', shape = 'batch')

SydneyBioX/scMerge documentation built on April 14, 2024, 3:22 a.m.