R: Simulate factor matrices and data using priors

simulate_whx {ccfindR}

R Documentation

Simulate factor matrices and data using priors

Description

Under Bayesian formulation, use prior distributions of factor matrices and generate simulated data

Usage

simulate_whx(nrow, ncol, rank, aw = 0.1, bw = 1, ah = 0.1, bh = 1)

Arguments

`nrow`	Number of features (genes).
`ncol`	Number of cells (samples).
`rank`	Rank (ncol of W, nrow of H).
`aw`	Shape parameter of basis prior.
`bw`	Mean of basis prior. Scale parameter is equal to `aw/bw`.
`ah`	Shape parameter of coefficient prior.
`bh`	Mean of coefficient prior. Scale parameter is equal to `ah/bh`.

Details

Basis W and coefficient matrices H are sampled from gamma distributions (priors) with shape (aw,ah) and mean (bw,bh) parameters. Count data X are sampled from Poisson distribution with mean values given by WH.

Value

List with elements w, h, and x, each containing basis, coefficient, and count matrices.

Examples

set.seed(1)
x <- simulate_whx(nrow=50,ncol=100,rank=5)
s <- scNMFSet(count=x$x)
s <- vb_factorize(s,ranks=seq(2,8),nrun=5)
plot(s)

[Package ccfindR version 1.7.0 Index]