get_params {polyester} | R Documentation

## Estimate zero-inflated negative binomial parameters from a real dataset

### Description

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.

### Usage

    get_params(counts, threshold = NULL)

### Arguments

`counts` | A matrix of counts. If you want to simulate from a ballgown object, see `fpkm_to_counts`
`threshold` | Only estimate parameters from transcripts with row means greater than threshold

### Value

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.

### Author(s)

Jeff Leek

### Examples

      library(ballgown)
      data(bg)
      countmat = fpkm_to_counts(bg, mean_rps=400000)
      params = get_params(countmat)

[Package polyester version 1.28.0 Index]