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Compute cell cluster markers.

Source: R/markers.R
scran_markers.Rd

This is a wrapper around scran::findMarkers(). Depending on test type, stats.* columns in returned DataFrame are replaced by either lfc_* or auc_*. DataFrames with results are appended to the params tibble, but because scran::findMarkers() returns DataFrame for each level of a factor, those are unnested in the returned tibble. That means for each row of params you will get result (row) for each tested level.

Usage

scran_markers(sce, params, markers_type = c("global", "contrast"))

Arguments

sce

A SingleCellExperiment object with normalized log-expression values and the following rowData() columns: "ENSEMBL", "ENTREZID", "SYMBOL", "GENENAME".

params

A tibble. See cluster_markers_test_params or contrasts_test_params target for details.

markers_type

A character scalar: type of markers to get. For "contrast", the following parameters are always used in scran::findMarkers():

  • direction = "any"

  • pval.type = "any"

  • min.prop = NULL

Value

A tibble.