classifyCellsAndDoublets: Classify cells to species

In rajewsky-lab/dropbead: dropbead

Description

Classify the cells to species according to the transcripts they express. The differentiation of species is performed internally and according to the species1 and species2 labels of the sample. If the classificiation is not confident enough, the cell is characterized as doublet.

Usage

classifyCellsAndDoublets(object, threshold = 0.9, min.trans = 500)

Arguments

object	A MixedSpeciesSample object.
threshold	The threshold which the ratio of transcripts of one species over the other has to surpass in order to succesfully assign a cell to a species. Below that threshold the cell is characterized as a doublet.
min.trans	The minimum number of transcripts (UMIs) required for a cell.

Value

A data.frame containing the cell barcodes, the number of transcripts per species and the characterization of the cell.

rajewsky-lab/dropbead documentation built on May 26, 2019, 10 p.m.