meta_genes {ccfindR} | R Documentation

## Find metagenes from basis matrix

### Description

Retrieve a basis matrix from an object and find metagenes.

### Usage

    meta_genes(object, rank, basis.matrix = NULL, max.per.cluster = 10,
      gene_names = NULL, subtract.mean = TRUE, log = TRUE)

### Arguments

`object` | Object of class `scNMFSet`.
`rank` | Rank value for which metagenes are to be found.
`basis.matrix` | Instead of an object containing basis matrices, the matrix itself can be provided.
`max.per.cluster` | Maximum number of metagenes per cluster.
`gene_names` | Names of genes to replace row names of basis matrix.
`subtract.mean` | Standardize the matrix elements with means within each row.
`log` | Use geometric mean and division instead of arithmetic mean and subtraction with `subtract.mean`.

### Value

List of vectors each containing metagene names of clusters.

### Examples

    set.seed(1)
    x <- simulate_data(nfeatures=10,nsamples=c(20,20,60))
    rownames(x) <- seq_len(10)
    colnames(x) <- seq_len(100)
    s <- scNMFSet(count=x,rowData=seq_len(10),colData=seq_len(100))
    s <- vb_factorize(s,ranks=seq(2,5))
    meta_genes(s, rank=4)

[Package ccfindR version 1.6.0 Index]