runSingleR {singleCellTK} | R Documentation |
SingleR works with a reference dataset where the cell type labeling is given. Given a reference dataset of samples (single-cell or bulk) with known labels, it assigns those labels to new cells from a test dataset based on similarities in their expression profiles.
runSingleR( inSCE, useAssay = "logcounts", useSCERef = NULL, labelColName = NULL, useBltinRef = c("hpca", "bpe", "mp", "dice", "immgen", "mouse", "zeisel"), level = c("main", "fine", "ont"), featureType = c("symbol", "ensembl"), labelByCluster = NULL )
inSCE |
SingleCellExperiment inherited object. Required. |
useAssay |
character. A string specifying which assay to use for expression profile identification. Required. |
useSCERef |
SingleCellExperiment inherited object. An
optional customized reference dataset. Default |
labelColName |
A single character. A string specifying the column in
|
useBltinRef |
A single character. A string that specifies a reference
provided by SingleR. Choose from |
level |
A string for cell type labeling level. Used only when using
some of the SingleR built-in references. Choose from |
featureType |
A string for whether to use gene symbols or Ensembl IDs
when using a SingleR built-in reference. Should be set based on the type of
|
labelByCluster |
A single character. A string specifying the column name
in |
Input SCE object with cell type labeling updated in
colData(inSCE)
, together with scoring metrics.
data("sceBatches") logcounts(sceBatches) <- log(counts(sceBatches) + 1) #sceBatches <- runSingleR(sceBatches, useBltinRef = "mp")