dada2.finish: Finish the dada2 pipeline

In kstagaman/sharpton-lab-dada2-pipeline: Provides Functions to Easily Replicate the Sharpton Lab dada2 Pipeline

Finish the dada2 pipeline

Description

This function completes the dada2 pipeline once the user has viewed the plots generated by dada2.upto.qualPlots and decided on the forward (and reverse) truncation lengths.

Usage

dada2.finish(
  fastq.path,
  truncFwd.len,
  truncRev.len,
  taxa.db,
  metadata.file,
  maxCores = 4,
  build.tree = TRUE,
  guide.seqs.file = NULL,
  alignment.template.file = NULL,
  fasttree.path = NULL,
  user.output.path = NULL,
  paired = TRUE,
  force = FALSE,
  ask = TRUE
)

Arguments

fastq.path	Path to raw FASTQ files. This should be the same path supplied to 'dada2.upto.qualPlots'.
truncFwd.len	Truncate forward reads after this many bases. Reads shorter than this are discarded.
truncRev.len	Truncate reverse reads after this many bases. Reads shorter than this are discarded.
taxa.db	Path to the database file to be used to assign taxonomy to the ASVs.
metadata.file	Path to file containing metadata for samples used in creating the output phyloseq object. Must be formatted as csv, tsv, or rds.
maxCores	The maximum number of cores to utilize in steps that are parallelizabe. Default is 4.
build.tree	Logical. Should a phylogenetic tree be created for the ASVs called by 'dada2'? Defalt is TRUE.
guide.seqs.file	(Optional) Path to file containing guide sequences for improved tree building. Only needed if above parameter 'build.tree' is TRUE AND you *do not* want to use the provided files. Default is NULL.
alignment.template.file	(Optional) Path to file containing aligment template used for NAST alignment of sequences prior to tree building. Only needed if above parameter 'build.tree' is TRUE AND you *do not* want to use the provided files. Default is NULL.
fasttree.path	(Optional) Path to FastTree executable. Only needed if above parameter 'build.tree' is TRUE.
user.output.path	Path to a directory if you want to use a specific output directory instead of the one programmatically generated by the pipeline. Primarily used if you are re-running a pipeline and want to save to previously generated output path. Default is NULL (which will autogenerate the output path).
paired	Logical. Are these paired sequence data? Default is TRUE.
force	Logical. By default the pipeline will skip steps if their corresponding output objects already exist. Set to TRUE to force the pipeline to run through all steps. Default is FALSE.
ask	Logical. Whether to prompt user to make a choice if sample names from file names don't match sample names from metadata file whether to proceed or not. Setting to FALSE means script will proceed only with the samples that are common to both. Default TRUE.

See Also

dada2, filterAndTrim, learnErrors, dada, mergePairs, removeBimeraDenovo, assignTaxonomy, phyloseq

kstagaman/sharpton-lab-dada2-pipeline documentation built on Sept. 24, 2022, 11:41 a.m.