meta_genes: Find metagenes from basis matrix

In ccfindR: Cancer Clone Finder

Description

Retrieve a basis matrix from an object and find metagenes.

Usage

meta_genes(object, rank, basis.matrix = NULL, max.per.cluster = 10,
  gene_names = NULL, subtract.mean = TRUE, log = TRUE)

Arguments

object	Object of class scNMFSet.
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 subtract.mean.

Value

List of vectors each containing metagene names of clusters.

Examples

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)

Example output

Rank = 2: Nsteps =34, log(evidence) =-3.718765, hyper = (0.3940387,4.846422,0.5103102,0.9926368), dispersion = 1
Rank = 3: Nsteps =150, log(evidence) =-2.757019, hyper = (0.2362899,3.123985,0.591215,1.058757), dispersion = 1
Rank = 4: Nsteps =174, log(evidence) =-2.819187, hyper = (0.1309591,2.420701,0.6631048,1.020508), dispersion = 1
Rank = 5: Nsteps =102, log(evidence) =-3.02615, hyper = (0.1439153,1.836899,0.7009927,1.088136), dispersion = 1
[[1]]
[1] "3"  "8"  "10" "7"  "1" 

[[2]]
[1] "9" "2" "4"

[[3]]
[1] "6"

[[4]]
[1] "5"

ccfindR documentation built on Nov. 8, 2020, 5:12 p.m.