checkZymoBiomics: Compare ZymoBiomics to Experimental

In microsud/chkMocks: Compare Mock Community Samples in Microbiome Sequencing Studies

Compare ZymoBiomics to Experimental

Description

Compare ZymoBiomics to Experimental

Usage

checkZymoBiomics(
  x,
  mock_db = NULL,
  multithread = 2,
  threshold = 60,
  verbose = FALSE,
  strand = "top",
  ...
)

Arguments

x	Phyloseq objects where taxa_names are ASV sequences
mock_db	ZymoTrainingSet
multithread	Passed on to DECIPHER::IdTaxa Default is NULL
threshold	Passed on to DECIPHER::IdTaxa. Default is 60
verbose	Default is FALSE
strand	DECIPHER::IdTaxa Default is top
...	Arguments to pass on to DECIPHER::IdTaxa

Details

Compare ZymoBiomics theoretical to Experimental composition.

Value

List with pseq, and cor table

Author(s)

Sudarshan Shetty [e-mail]

Examples

library(phyloseq)

output.dat <- checkZymoBiomics(ZymoExamplePseq,
                               mock_db = ZymoTrainingSet,
                               multithread= 2,
                               threshold = 80,
                               strand = "top",
                               verbose = FALSE)

microsud/chkMocks documentation built on July 1, 2023, 9:23 p.m.