meta_genes: Find metagenes from basis matrix

Description Usage Arguments Value Examples

View source: R/utils.R

Description

Retrieve a basis matrix from an object and find metagenes.

Usage

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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

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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.