assignTaxonomyCustomMock: Assign Custom Mocks Taxonomy

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

Assign Custom Mocks Taxonomy

Description

Assign Custom Mocks Taxonomy

Usage

assignTaxonomyCustomMock(
  x,
  mock_db = NULL,
  processors = NULL,
  threshold = 60,
  strand = "top",
  verbose = FALSE,
  ...
)

Arguments

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

Details

For consistency in taxonomic assignments, use only a small database that has 16S rRNA gene sequences from mock community genomes. This is done to avoid any clashes/changes that happen with public databases and to get a direct comparison.

Value

Phyloseq with new taxonomy

Author(s)

Sudarshan Shetty [e-mail]

Examples

#output.dat <- assignTaxonomyCustomMock(ps.zym,
 #                                      mock_db = NULL,
  #                                     processors = 2,
   #                                    threshold = 80)

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