CorrelateReference: Correlate all reference profiles to each other using...

In jdekanter/CHETAH: Fast and accurate scRNA-seq cell type identification

Description

Correlate all reference profiles to each other using differentially expressed genes.

Usage

CorrelateReference(ref_cells = NULL, ref_profiles = NULL,
  ref_ct = "celltypes", ref_c = NA, return = FALSE, n_genes = 200,
  fix_ngenes = TRUE, print_steps = FALSE, only_pos = FALSE)

Arguments

ref_cells	the reference, similar to CHETAHclassifier's ref_cells
ref_profiles	similar to CHETAHclassifier's ref_profiles
ref_ct	the colData of ref_cells where the cell types are stored.
ref_c	the assay of ref_cells to use
return	return the matrix that was used to produce the plot
n_genes	as in CHETAHclassifier
fix_ngenes	as in CHETAHclassifier
print_steps	as in CHETAHclassifier
only_pos	as in CHETAHclassifier

Value

A square plot. The values show how much two reference profiles correlate, when using the genes with the highest fold-change.

Examples

CorrelateReference(ref_cells = headneck_ref)

jdekanter/CHETAH documentation built on Sept. 20, 2019, 3:31 a.m.