dada2.upto.qualPlots: Dada2 up to Quality Plots

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

Dada2 up to Quality Plots

Description

This function runs the first part of the pipeline, up through making quality plots, allowing the user to manually choose the truncation lengths based on those results.

Usage

dada2.upto.qualPlots(
  fastq.path,
  file.split.pattern = "--",
  maxCores = 4,
  random.seed = 42,
  user.output.path = NULL,
  force = FALSE,
  ask = TRUE
)

Arguments

fastq.path	Path to raw FASTQ files.
file.split.pattern	A character string containg the pattern you want to use to separate the sample name and R1/R2 in the symlink names. Default is '–'.
maxCores	The maximum number of cores to utilize in steps that are parallelizabe. Default is 4.
random.seed	A integer utilized by 'set.seed' to make pipeline reproducible
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 verify files in 'fastq.path'. FALSE skips this verification. Default TRUE.
user.out.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).

See Also

dada2, plotQualityProfile

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