scoreCells: Classify cells using marker genes.

Description Usage Arguments Value

Description

Classify cells using marker genes.

Usage

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scoreCells(dataset, markerGenes = NULL, geneColumn = "entrez_id",
  scoreColumn = "score", classColumn = "cell_type")

Arguments

dataset

A FASTGenomics Matrix of expression values.

markerGenes

An optional data frame with scores of marker genes for cell types; the immune cell markers compiled from Newman et al., Nature Methods (2015) is provided as default.

geneColumn

Gene column name in markerGenes data frame; defaults to entrez_id.

scoreColumn

Score column name in markerGenes data frame; defaults to score.

classColumn

Class column name in markerGenes data frame; defaults to cell_type.

Value

A data frame with class assignment and scores for classes per cell.


clajusch/ClEvaR documentation built on May 9, 2019, 4:55 a.m.