parEstimate: Parameter estimation in Dirichlet-multinomial distribution

In markrobinsonuzh/treeAGG: Tree Aggregation

Description

parEstimate is a wrapper function generated from the function dirmult with default setting on init, initscalar, epsilon, trace and mode. It allows the input data to accept matrix or leafSummarizedExperiment and output the value pi and theta.

Usage

parEstimate(data)

Arguments

data	A matrix or leafSummarizedExperiment. Samples in the columns and entities in the rows.

Value

A list including “pi” and “theta”

Author(s)

Ruizhu Huang

Examples

library(S4Vectors)
set.seed(1)
y <- matrix(rnbinom(100,size=1,mu=10),nrow=10)
colnames(y) <- paste("S", 1:10, sep = "")
rownames(y) <- tinyTree$tip.label


toy_lse <- leafSummarizedExperiment(tree = tinyTree,
                                    assays = list(y))
res <- parEstimate(data = toy_lse)

metadata(res)$assays.par

markrobinsonuzh/treeAGG documentation built on May 26, 2019, 9:32 a.m.