EstPrior: Estimate size and mu for Negative Binomial distribution for...

In WT215/bayNorm: Single-cell RNA sequencing data normalization

Estimate size and mu for Negative Binomial distribution for each gene using MME method

Description

Input raw data and return estimated size and mu for each gene using the MME method.

Usage

EstPrior(Data, verbose = TRUE)

Arguments

Data	A matrix of single-cell expression where rows are genes and columns are samples (cells). Data can be of class SummarizedExperiment (the assays slot contains the expression matrix, is named "Counts"), just matrix or sparse matrix.
verbose	print out status messages. Default is TRUE.

Details

mu and size are two parameters of the prior that need to be specified for each gene in bayNorm. They are parameters of negative binomial distribution. The variance is mu + mu^2/size in this parametrization.

Value

List containing estimated mu and size for each gene.

Examples

data('EXAMPLE_DATA_list')
#Return estimated mu and size for each gene using MME method.
MME_est<-EstPrior(Data=EXAMPLE_DATA_list$inputdata[,seq(1,30)],
verbose=TRUE)

WT215/bayNorm documentation built on Sept. 2, 2022, 1:46 a.m.