fineTuningRound: Internal function for a step in the fine-tuning process

In dviraran/SingleR: Reference-based single-cell RNA-seq annotation

Description

Internal function for a step in the fine-tuning process

Usage

fineTuningRound(topLabels, types, ref_data, genes, mat, sd.thres, sc_data,
  quantile.use, fine.tune.thres)

Arguments

topLabels	list of the cell type to use in the fine-tuning round
types	list of all cell types
ref_data	the reference expression data
genes	list of genes to use for the analysis, or 'de' or 'sd'
mat	the median expression matrix for the reference
sd.thres	the standard deviation threshold to use for choosing genes. Only used if genes == 'sd'
sc_data	the single cell data
quantile.use	the quantile for the aggregating scores
fine.tune.thres	a threshold of top cell types to use for the next round.

Value

the cell types to use for the next round or one cell type which is the final annotation.

dviraran/SingleR documentation built on April 21, 2020, 3:23 p.m.