SingleR {SingleR} | R Documentation

## Annotate scRNA-seq data

### Description

Returns the best annotation for each cell in a test dataset, given a labelled reference dataset in the same feature space.

### Usage

    SingleR(
      test,
      ref,
      labels,
      method = NULL,
      clusters = NULL,
      genes = "de",
      sd.thresh = 1,
      de.method = "classic",
      de.n = NULL,
      de.args = list(),
      aggr.ref = FALSE,
      aggr.args = list(),
      recompute = TRUE,
      restrict = NULL,
      quantile = 0.8,
      fine.tune = TRUE,
      tune.thresh = 0.05,
      prune = TRUE,
      assay.type.test = "logcounts",
      assay.type.ref = "logcounts",
      check.missing = TRUE,
      BNPARAM = KmknnParam(),
      BPPARAM = SerialParam()
    )

### Arguments

`test` | A numeric matrix of single-cell expression values where rows are genes and columns are cells. Alternatively, a SummarizedExperiment object containing such a matrix.
`ref` | A numeric matrix of (usually log-transformed) expression values from a reference dataset, or a SummarizedExperiment object containing such a matrix; see `trainSingleR` for details. Alternatively, a list or List of SummarizedExperiment objects or numeric matrices containing multiple references. Row names may be different across entries but only the intersection will be used, see Details.
`labels` | A character vector or factor of known labels for all samples in `ref`. Alternatively, if `ref` is a list, `labels` should be a list of the same length. Each element should contain a character vector or factor specifying the label for the corresponding entry of `ref`.
`method` | Deprecated.
`clusters` | A character vector or factor of cluster identities for each cell in `test`. If set, annotation is performed on the aggregated cluster profiles, otherwise it defaults to per-cell annotation.
`genes, sd.thresh, de.method, de.n, de.args` | Arguments controlling the choice of marker genes used for annotation, see `trainSingleR`.
`aggr.ref, aggr.args` | Arguments controlling the aggregation of the references prior to annotation, see `trainSingleR`.
`recompute` | Logical scalar indicating whether to set up indices for later recomputation of scores, when `ref` contains multiple references from which the individual results are to be combined. (See the difference between `combineCommonResults` and `combineRecomputedResults`.)
`restrict` | A character vector of gene names to use for marker selection. By default, all genes in `ref` are used.
`quantile, fine.tune, tune.thresh, prune` | Further arguments to pass to `classifySingleR`.
`assay.type.test` | An integer scalar or string specifying the assay of `test` containing the relevant expression matrix, if `test` is a SummarizedExperiment object.
`assay.type.ref` | An integer scalar or string specifying the assay of `ref` containing the relevant expression matrix, if `ref` is a SummarizedExperiment object (or is a list that contains one or more such objects).
`check.missing` | Logical scalar indicating whether rows should be checked for missing values (and if found, removed).
`BNPARAM` | A BiocNeighborParam object specifying the algorithm to use for building nearest neighbor indices.
`BPPARAM` | A BiocParallelParam object specifying how parallelization should be performed, if any.

### Details

This function is just a convenient wrapper around `trainSingleR` and `classifySingleR`. The function will automatically restrict the analysis to the intersection of the genes in both `ref` and `test`. If this intersection is empty (e.g., because the two datasets use different gene annotations), an error will be raised.

If `clusters` is specified, per-cell profiles are summed to obtain per-cluster profiles. Annotation is then performed by running `classifySingleR` on these profiles. This yields a DataFrame with one row per level of `clusters`.

The default settings of this function are based on the assumption that `ref` contains or bulk data. If it contains single-cell data, this usually requires a different `de.method` choice. Read the Note in `?trainSingleR` for more details.

### Value

A DataFrame is returned containing the annotation statistics for each cell (one cell per row). This is identical to the output of `classifySingleR`.

### Author(s)

Aaron Lun, based on code by Dvir Aran.

### References

Aran D, Looney AP, Liu L et al. (2019). Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat. Immunology 20, 163–172.

### Examples

    # Mocking up data with log-normalized expression values:
    ref <- .mockRefData()
    test <- .mockTestData(ref)

    ref <- scuttle::logNormCounts(ref)
    test <- scuttle::logNormCounts(test)

    # Running the classification with different options:
    pred <- SingleR(test, ref, labels=ref$label)
    table(predicted=pred$labels, truth=test$label)

    k.out<- kmeans(t(assay(test, "logcounts")), center=5) # mock up a clustering
    pred2 <- SingleR(test, ref, labels=ref$label, clusters=k.out$cluster)
    table(predicted=pred2$labels, cluster=rownames(pred2))

[Package SingleR version 1.8.1 Index]