tagData: Finds cell type markers for a matrix of pure cell type...

In mchikina/CellCODE: Cell type COmputational Differential Estimation.

Usage

tagData(data, cutoff = 2, max = NULL, ref = NULL, ref.mean = F)

Arguments

data	Pure cell expression data. Each column represents a unique cell type.
cutoff	In order to be considered a marker gene the gene's expression in a single cell type must exceed all other cell types by this amount.
max	The maximum number of marker genes to return. The most highly expressed genes are picked from the set of eligible genes.
ref	A reference dataset. This dataset is used to filter the set of genes so that every marker gene is present in the reference dataset
ref.mean	Use the reference dataset to define genes expression levels. With this option which marker genes are returned (if max is set to a number) is based on their expression in the reference dataset and not the pure cell dataset. Can be useful if the absolute expression levels in the pure cell dataset are unreliable.

mchikina/CellCODE documentation built on May 23, 2019, 1:13 p.m.