psBlockResults: psBlockResults

In PratheepaJ/BARBI: A Bayesian Approach to Contamination Removal in Molecular Microbial Studies

Description

Prepare the phyloseq object for the Bayesian inference

Usage

psBlockResults(
  ps,
  sampleTypeVar = "Sample_Type",
  caselevels = "Plasma",
  controllevel = "Control",
  sampleName = "SampleCode",
  blockVar = "block"
)

Arguments

ps	phyloseq object.
sampleTypeVar	character, variable defines the specimen samples and control samples in the sample data of phyloseq.
caselevels	character vector, levels (types) of the specimen-samples, e.g. 'healthy plasma' and 'sick plasma'.
controllevel	character, level of the control samples, e.g. 'control'
sampleName	character, variable defines the sample names in the sample data of phyloseq. This should match sample_names() of phyloseq.
blockVar	character, variable defines the block of the samples in the sample data of phyloseq. If there is only one block, you need to create a variable with only one level.

Value

A list of phyloseq objects, phyloseq of negative control samples by block, phyloseq of taxa with prevalence zero in negative control samples by block, phyloseq of specimen-samples by block.

PratheepaJ/BARBI documentation built on April 16, 2020, 11:51 a.m.