splatEstOutlier: Estimate Splat expression outlier parameters
In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

splatEstOutlier

R Documentation

Estimate Splat expression outlier parameters

Description

Parameters are estimated by comparing means of individual genes to the median mean expression level.

Usage

splatEstOutlier(norm.counts, params)

Arguments

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

Details

Expression outlier genes are detected using the Median Absolute Deviation (MAD) from median method. If the log2 mean expression of a gene is greater than two MADs above the median log2 mean expression it is designated as an outlier. The proportion of outlier genes is used to estimate the outlier probability. Factors for each outlier gene are calculated by dividing mean expression by the median mean expression. A log-normal distribution is then fitted to these factors in order to estimate the outlier factor location and scale parameters using fitdist.