meta_genes {ccfindR} | R Documentation |
Retrieve a basis matrix from an object and find metagenes.
meta_genes(object, rank, basis.matrix = NULL, max.per.cluster = 10, gene_names = NULL, subtract.mean = TRUE, log = TRUE)
object |
Object of class |
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 |
List of vectors each containing metagene names of clusters.
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)