meta_gene.cv: Meta gene table with CV

In hjunwoo/ccfindR: Cancer Clone Finder

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 = Inf)

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)

hjunwoo/ccfindR documentation built on Oct. 4, 2019, 10:31 a.m.