meta_gene.cv {ccfindR} | R Documentation |
Generates meta gene table with coefficient of variation
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)
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
|
dbasis |
Variance of basis matrix. Only necessary when
|
max.per.cluster |
Maximum meta genes per cluster. |
gene_names |
Name of genes. If |
subtract.mean |
Standardize magnitudes of basis elements by subtracting mean |
log |
Use geometric mean. |
cv.max |
Upper bound for CV in selecting meta genes. |
Data frame with meta genes and their CV in each column.
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)