create_read_numbers: Generate a simulated data set based on known model parameters
In alyssafrazee/polyester-release: Simulate RNA-seq reads

Description Usage Arguments Value Author(s) Examples

Generate a simulated data set based on known model parameters

1 2	create_read_numbers(mu, fit, p0, m = NULL, n = NULL, mod = NULL, beta = NULL, seed = NULL)

`mu`	Baseline mean expression for negative binomial model
`fit`	Fitted relationship between log mean and log size
`p0`	A vector of the probabilities a count is zero
`m`	Number of genes/transcripts to simulate (not necessary if mod, beta are specified)
`n`	Number of samples to simulate (not necessary if mod, beta are specified)
`mod`	Model matrix you would like to simulate from without an intercept
`beta`	set of coefficients for the model matrix (must have same number of columns as mod)
`seed`	optional seed to set (for reproducibility)

counts Data matrix with counts for genes in rows and samples in columns

Jeff Leek

library(ballgown)
  data(bg)
  countmat = fpkm_to_counts(bg, mean_rps=400000)
  params = get_params(countmat)
  Ntranscripts = 50
  Nsamples = 10
  custom_readmat = create_read_numbers(mu=params$mu, fit=params$fit,
    p0=params$p0, m=Ntranscripts, n=Nsamples, seed=103)