splatEstDropout: Estimate Splat dropout parameters

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

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.

Value

SplatParams object with estimated values.

Oshlack/splatter documentation built on April 1, 2024, 9:37 a.m.