setFastPaired: Create a fastPaired object
In ananata/fastq2otu: FASTQ2OTU: Automate microbiome analyses

Create a fastPaired object

setFastPaired(
  inDir,
  outDir,
  validate = TRUE,
  pattern = ".*_[1,2].fastq(.gz)?",
  mergeSeqs = TRUE,
  trimOverhang = FALSE,
  minOverlap = 12,
  maxMismatch = 0,
  returnRejects = FALSE,
  justConcatenate = FALSE,
  verbose = FALSE,
  prefix = "myproject",
  isPaired = TRUE,
  derepN = 1e+06,
  getErrPDF = FALSE,
  errN = 1e+08,
  multithread = FALSE,
  dadaBandSize = 16,
  dadaOmegaA = 1e-40,
  getChimeraTable = FALSE,
  minSampleFraction = 0.9,
  ignoreNegatives = 1,
  minFoldParentOverAbundance = 1.5,
  detectionAbundance = 2,
  allowOneOff = FALSE,
  maxShift = 16,
  downloadSeqs = FALSE,
  trimAdapters = FALSE,
  generateReport = FALSE
)

`inDir`	Required input. Path to FASTQ files.
`outDir`	Required input. Path to write output files.
`validate`	Default is TRUE. Execute all validation methods.
`pattern`	Regex pattern used to select fastq files from directory.
`mergeSeqs`	Required input. Default is TRUE to merge forward and reverse amplicons. FALSE prevents DADA2's mergePairs method from being executed.
`trimOverhang`	Default is FALSE. Sets trimOverhang parameter for DADA2's mergePairs method.
`minOverlap`	Default is 12. Sets minOverlap parameter for DADA2's mergePairs function.
`maxMismatch`	Default is 0. Sets maxMismatch parameter for DADA2's mergePairs method.
`returnRejects`	Default is FALSE. Sets returnRejects paramater for DADA2's mergePairs method.
`justConcatenate`	Default is FALSE. Sets returnRejects paramater for DADA2's mergePairs method.
`verbose`	Default is FALSE. Sets verbose parameter for DADA2 methods.
`prefix`	Default is "myproject". Project-specific label that will be included in the names of all files and directories created.
`isPaired`	Default is TRUE for fastPaired object. If FALSE, a fastSingle object will be created instead.
`derepN`	Default is 1e+06. Sets the sampling parameter for DADA2's derepFastq method.
`getErrPDF`	Default is FALSE. If TRUE a learn errors plot from DADA's plotErrors method is produced.
`errN`	Default is 1e+08. Sets the nbases parameter for DADA2's learnErrors method.
`multithread`	Default is FALSE. Sets multithread parameter for DADA2 methods.
`dadaBandSize`	Default is 16. Sets the BAND_SIZE parameter for DADA2's dada method.
`dadaOmegaA`	Default is 1e-40. Sets the OMEGA_A paramter for DADA2's dada method.
`getChimeraTable`	Default is FALSE. When TRUE, creates table showing all sequences labled as chimeric by DADA2 (uses DADA2's isBimeraDevovoTable function as opposed to removeBimeraDenovo).
`minSampleFraction`	Default is 0.9. Sets minDetection parameter for DADA2's removeBimeraDenovo and isBimera functions.
`ignoreNegatives`	Default is 1. Sets ignoreNegatives parameter for DADA2's removeBimeraDenovo and isBimera functions.
`minFoldParentOverAbundance`	Default is 1.5. Sets minfoldParentOverabundance parameter for DADA2's removeBimeraDenovo and isBimera functions.
`detectionAbundance`	Default is 2. Sets detectionParentAbundace parameter for DADA2's removeBimeraDenovo and isBimera functions.
`allowOneOff`	Default is FALSE. Sets allowOneOff parameter for DADA2's removeBimeraDenovo and isBimera functions.
`maxShift`	Default is 16. Sets maxShift parameter for DADA2's removeBimeraDenovo and isBimera functions.
`generateReport`	Default is FALSE. If TRUE, a fastReport object will be created when runPipeline is executed.
`downloadSeqs.`	Default is FALSE. If TRUE, a fastSeqDump object will be created when runPipeline method is executed.
`trimAdapters.`	Default is FALSE. If TRUE, a fastPrimerTrim object will be created when runPipeline method is executed.