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 1.3.0 Index]