Marker Enrichment Modeling — altmem • altmem

A wrapper around cytoMEM::MEM() that accepts a matrix, data frame, SummarizedExperiment, or SingleCellExperiment, and supports non-numeric cluster labels.

Usage

altmem(
  x,
  cluster_col,
  assay_name = "exprs",
  markers = "all",
  transform = FALSE,
  cofactor = 1,
  choose.markers = FALSE,
  choose.ref = FALSE,
  zero.ref = FALSE,
  IQR.thresh = NULL
)

Arguments

x: A matrix, data frame, SummarizedExperiment, or SingleCellExperiment.
cluster_col: Name of the column containing cluster labels.
assay_name: Name of the assay to use for the expression matrix. Only used for SummarizedExperiment input. Defaults to "exprs".
markers: Character vector of marker names to include, or "all" to use all markers.
transform, cofactor, choose.markers, choose.ref, zero.ref, IQR.thresh: Passed to cytoMEM::MEM().

Value

A list of matrices (the return value of cytoMEM::MEM()).