Align the single cell RNAseq data to codex data

Align the scRNA-seq Seurat object to the Codex data by the classifer trained from the scRNA-seq Seurat object by buildClassifierFromSeurat

alignScRNAseqToCodex(
  codexSeu,
  scSeu,
  classifier,
  newAssayName = "aligned",
  assay = "RNA"
)

Arguments

codexSeu

The Codex Seurat object

scSeu

The single cell RAN-seq Seurat object

classifier

A KNN classifer created from the scRNA-seq Seurat object by buildClassifierFromSeurat

assay, newAssayName

The assay name for single cell RNAseq expressions.

Value

An aligned Seurat object.

Examples

if (FALSE) { # \dontrun{
markers <- readRDS(system.file('extdata', 'markers.name.map.rds',
package='cdQuPath'))
pseudo <- readRDS(system.file('extdata', 'pseudobulk.scRNAseq.rds',
package='cdQuPath'))
classifier <- buildClassifierFromSeurat(pseudo, markers)
tsv <- system.file("extdata", "test.qptiff.tsv.zip",
                   package = "cdQuPath",
                   mustWork = TRUE)
seu <- createSeuratObj(tsv, useValue = 'Median',
                       markerLocations = CodexPredefined$markerLocations)
seu <- fitGMM(seu)
alignedPseudo <- alignScRNAseqToCodex(codexSeu = seu,
                    scSeu = pseudo,
                    classifier = classifier)
} # }