splatEstDropout: Estimate Splat dropout parameters
In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

splatEstDropout

R Documentation

Estimate Splat dropout parameters

Description

Estimate the midpoint and shape parameters for the logistic function used when simulating dropout.

Usage

splatEstDropout(norm.counts, params)

Arguments

`norm.counts`	library size normalised counts matrix.
`params`	SplatParams object to store estimated values in.

Details

Logistic function parameters are estimated by fitting a logistic function to the relationship between log2 mean gene expression and the proportion of zeros in each gene. See nls for details of fitting. Note this is done on the experiment level, more granular (eg. group or cell) level dropout is not estimated.