estimateBetaParamsFromCounts: Estimate parameters of a Beta distribution from counts

In Oshlack/speckle: Statistical methods for analysing single cell RNA-seq data

Estimate parameters of a Beta distribution from counts

Description

This function estimates the two parameters of the Beta distribution, alpha and beta for each cell type. The input is a matrix of cell type counts, where the rows are the cell types/clusters and the columns are the samples.

Usage

estimateBetaParamsFromCounts(x)

Arguments

x	a matrix of counts

Details

This function is called from the plotting function plotCellTypeMeanVar in order to estimate the variance for the Beta-Binomial distribution for each cell type.

Value

outputs a list object with the following components

n	Normalised library size
alpha	a vector of alpha parameters for the Beta distribution for each cell type
beta	vector of beta parameters for the Beta distribution for each cell type
pi	Estimate of the true proportion for each cell type
dispersion	Dispersion estimates for each cell type
var	Variance estimates for each cell type

Author(s)

Belinda Phipson

Examples

data <- speckle_example_data()
x <- table(data$clusters, data$samples)
estimateBetaParamsFromCounts(x)

Oshlack/speckle documentation built on Oct. 16, 2022, 9:39 a.m.