get_params {polyester} | R Documentation |
This function estimates the parameters of a zero inflated negative binomial distribution based on a real count data set based on the method of moments. The function also returns a spline fit of log mean to log size which can be used when generating new simulated data.
get_params(counts, threshold = NULL)
counts |
A matrix of counts. If you want to simulate from a ballgown
object, see |
threshold |
Only estimate parameters from transcripts with row means greater than threshold |
p0 A vector of probabilities that the count will be zero, one for each gene/transcript.
mu The estimated negative binomial mean by method of moments for the non-zero counts
size The estimated negative binomial size by method of moments for the non-zero counts
fit A fit relating log mean to log size for use in simulating new data.
Jeff Leek
library(ballgown) data(bg) countmat = fpkm_to_counts(bg, mean_rps=400000) params = get_params(countmat)