scMerge: Perform the scMerge algorithm

View source: R/scMerge.R

scMergeR Documentation

Perform the scMerge algorithm

Description

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

Usage

scMerge(
  sce_combine,
  ctl = NULL,
  kmeansK = NULL,
  exprs = "logcounts",
  hvg_exprs = "counts",
  batch_name = "batch",
  marker = NULL,
  marker_list = NULL,
  ruvK = 20,
  replicate_prop = 1,
  cell_type = NULL,
  cell_type_match = FALSE,
  cell_type_inc = NULL,
  BSPARAM = ExactParam(),
  svd_k = 50,
  dist = "cor",
  WV = NULL,
  WV_marker = NULL,
  BPPARAM = SerialParam(),
  return_all_RUV = FALSE,
  assay_name = NULL,
  plot_igraph = TRUE,
  verbose = FALSE
)

Arguments

sce_combine

A SingleCellExperiment object contains the batch-combined matrix with batch info in colData.

ctl

A character vector of negative control. It should have a non-empty intersection with the rows of sce_combine.

kmeansK

A vector indicates the kmeans's K for each batch. The length of kmeansK needs to be the same as the number of batch.

exprs

A string indicating the name of the assay requiring batch correction in sce_combine, default is logcounts.

hvg_exprs

A string indicating the assay that to be used for highly variable genes identification in sce_combine, default is counts.

batch_name

A character indicating the name of the batch column, default to "batch"

marker

An optional vector of markers, to be used in calculation of mutual nearest cluster. If no markers input, highly variable genes will be used instead.

marker_list

An optional list of markers for each batch, which will be used in calculation of mutual nearest cluster.

ruvK

An optional integer/vector indicating the number of unwanted variation factors that are removed, default is 20.

replicate_prop

A number indicating the ratio of cells that are included in pseudo-replicates, ranges from 0 to 1. Default to 1.

cell_type

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.

cell_type_match

An optional logical input for whether to find mutual nearest cluster using cell type information.

cell_type_inc

An optional vector indicating the indices of the cells that will be used to supervise the pseudo-replicate procedure.

BSPARAM

A BiocSingularParam class object from the BiocSingular package is used. Default is ExactParam().

svd_k

If BSPARAM is set to RandomParam or IrlbaParam class from BiocSingular package, then svd_k will be used to used to reduce the computational cost of singular value decomposition. Default to 50.

dist

The distance metrics that are used in the calculation of the mutual nearest cluster, default is Pearson correlation.

WV

A optional vector indicating the wanted variation factor other than cell type info, such as cell stages.

WV_marker

An optional vector indicating the markers of the wanted variation.

BPPARAM

A BiocParallelParam class object from the BiocParallel package is used. Default is SerialParam().

return_all_RUV

If FALSE, then only returns a SingleCellExperiment object with original data and one normalised matrix. Otherwise, the SingleCellExperiment object will contain the original data and one normalised matrix for each ruvK value. In this latter case, assay_name must have the same length as ruvK.

assay_name

The assay name(s) for the adjusted expression matrix(matrices). If return_all_RUV = TRUE assay_name must have the same length as ruvK.

plot_igraph

If TRUE, then during the un/semi-supervised scMerge, igraph plot will be displayed

verbose

If TRUE, then all intermediate steps will be shown. Default to FALSE.

Value

Returns a SingleCellExperiment object with following components:

  • assays: the original assays and also the normalised matrix

  • metadata: containing the ruvK vector, ruvK_optimal based on F-score, and the replicate matrix

Author(s)

Yingxin Lin, Kevin Wang

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
sce_mESC <- scMerge(sce_combine = example_sce,
ctl = segList_ensemblGeneID$mouse$mouse_scSEG,
kmeansK = c(3, 3),
assay_name = 'scMerge')

sce_mESC = scater::runPCA(sce_mESC, exprs_values = "logcounts")                      
scater::plotPCA(sce_mESC, colour_by = 'cellTypes', shape = 'batch')

sce_mESC = scater::runPCA(sce_mESC, exprs_values = 'scMerge')                                       
scater::plotPCA(sce_mESC, colour_by = 'cellTypes', shape = 'batch')

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