setFastAssignTaxa: Create a fastAssignTaxa object

In ananata/fastq2otu: FASTQ2OTU: Automate microbiome analyses

Description

Create a fastAssignTaxa object

Usage

setFastAssignTaxa(
  refDatabase,
  prefix = "myproject",
  validate = FALSE,
  minBootstrap = 50,
  tryComplement = FALSE,
  showBootstraps = FALSE,
  taxLevels = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  verbose = FALSE,
  multithread = FALSE
)

Arguments

refDatabase	Required input. Path to fasta-formatted database containing reference sequences used during taxonomic assignment.
prefix	Default is "myproject". Project-specific label that will be included in the names of all files and directories created.
validate	Default is FALSE. When TRUE all validation methods are executed.
minBootstrap	Default is 50. Sets min-bootstrap value for DADA2 assignTaxonomy method.
tryComplement	Default is FALSE. Sets value for tryComplement parameter for DADA2's assignTaxonomy method.
showBootstraps	Default is FALSE. Sets value for showBootstraps parameter for DADA2's assignTaxonomy method.
taxLevels	Provide character list of taxonomic levels to include in taxonomy assignment. The default OTU table generated from this function includes assignments from kingdom to species.
verbose	Default is FALSE. Sets verbose parameter for DADA2 methods.
multithread	Default is FALSE. Sets multithread parameter for DADA2 methods. TODO: Add Example

ananata/fastq2otu documentation built on Feb. 2, 2022, 4:20 p.m.