meta_gene.cv {ccfindR} | R Documentation

## Meta gene table with CV

### Description

Generates meta gene table with coefficient of variation

### Usage

    meta_gene.cv(object = NULL, rank, basis.matrix = NULL, dbasis = NULL,
      max.per.cluster = 100, gene_names = NULL, subtract.mean = TRUE,
      log = TRUE, cv.max = 1)

### Arguments

`object` | Main object containing factorization outcome
`rank` | Rank for which meta gene is to be found
`basis.matrix` | Basis matrix to work with. Only necessary when `object` is `NULL`.
`dbasis` | Variance of basis matrix. Only necessary when `object` is `NULL`.
`max.per.cluster` | Maximum meta genes per cluster.
`gene_names` | Name of genes. If `NULL`, will be taken from row names.
`subtract.mean` | Standardize magnitudes of basis elements by subtracting mean
`log` | Use geometric mean.
`cv.max` | Upper bound for CV in selecting meta genes.

### Value

Data frame with meta genes and their CV in each column.

### Examples

    set.seed(1)
    x <- simulate_whx(nrow=50, ncol=100, rank=5)
    s <- scNMFSet(x$x)
    s <- vb_factorize(s, ranks=seq(2,8), nrun=5)
    plot(s)
    meta_gene.cv(s, rank=5)

[Package ccfindR version 1.4.2 Index]