posteriorProbs: Access the posterior probabilities that results from analysis

In metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

Description

Accessing the posterior probabilities following a run through fitZig

Usage

posteriorProbs(obj)

Arguments

obj	a MRexperiment object.

Value

Matrix of posterior probabilities

Author(s)

Joseph N. Paulson

Examples

# This is a simple demonstration 
data(lungData)
k = grep("Extraction.Control",pData(lungData)$SampleType)
lungTrim = lungData[,-k]
k = which(rowSums(MRcounts(lungTrim)>0)<30)
lungTrim = cumNorm(lungTrim)
lungTrim = lungTrim[-k,]
smokingStatus = pData(lungTrim)$SmokingStatus
mod = model.matrix(~smokingStatus)
# The maxit is not meant to be 1 -- this is for demonstration/speed
settings = zigControl(maxit=1,verbose=FALSE)
fit = fitZig(obj = lungTrim,mod=mod,control=settings)
head(posteriorProbs(lungTrim))

metagenomeSeq documentation built on Nov. 8, 2020, 5:34 p.m.