CorrelateReference {CHETAH}R Documentation

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

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)

[Package CHETAH version 1.0.3 Index]