create_read_numbers: Generate a simulated data set based on known model parameters

In mikelove/polyesterAlpineMs: Simulate RNA-seq reads

Description

Generate a simulated data set based on known model parameters

Usage

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

Arguments

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)

Value

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

Author(s)

Jeff Leek

Examples

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)

mikelove/polyesterAlpineMs documentation built on May 22, 2019, 10:52 p.m.