getAdjustedMat: getAdjustedMat

In SydneyBioX/scMerge: scMerge: Merging multiple batches of scRNA-seq data

getAdjustedMat

Description

Get Adjusted Matrix with scMerge2 parameter estimated

Usage

getAdjustedMat(
  exprsMat,
  fullalpha,
  ctl = rownames(exprsMat),
  adjusted_means = NULL,
  ruvK = 20,
  return_subset_genes = NULL
)

Arguments

exprsMat	A gene (row) by cell (column) matrix to be adjusted.
fullalpha	A matrix indicates the estimated alpha returned by scMerge2().
ctl	A character vector of negative control. It should have a non-empty intersection with the rows of exprsMat.
adjusted_means	A rowwise mean of the gene by cell matrix
ruvK	An integer indicates the number of unwanted variation factors that are removed, default is 20.
return_subset_genes	An optional character vector of indicates the subset of genes will be adjusted.

Value

Returns the adjusted matrix will be return.

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)
scMerge2_res <- scMerge2(exprsMat = logcounts(example_sce),
batch = example_sce$batch,
ctl = segList_ensemblGeneID$mouse$mouse_scSEG,
return_matrix = FALSE)
cosineNorm_mat <- batchelor::cosineNorm(logcounts(example_sce))
adjusted_means <- DelayedMatrixStats::rowMeans2(cosineNorm_mat)
newY <- getAdjustedMat(cosineNorm_mat, scMerge2_res$fullalpha,
              ctl = segList_ensemblGeneID$mouse$mouse_scSEG,
              ruvK = 20,
              adjusted_means = adjusted_means)
assay(example_sce, "scMerge2") <- 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.