scran_markers: Compute cell cluster markers.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Compute cell cluster markers.

Description

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.

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.