meta_gene.cv: Meta gene table with CV

Description Usage Arguments Value Examples

View source: R/utils2.R

Description

Generates meta gene table with coefficient of variation

Usage

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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

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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.