dada2_raw_read_setup: dada2_raw_read_setup
In padpadpadpad/MicrobioUoE: R package for making our life easier

Description Usage Arguments Details Value Author(s)

Function to setup the workspace for the AB_dada2_pipeline

dada2_raw_read_setup(
  packages = c("ggplot2", "dada2", "phyloseq", "DECIPHER", "tidyr", "dplyr",
    "MicrobioUoE"),
  raw_path = "data/raw_fastq",
  filt_path = "data/filtered_fastq",
  plot_path = "plots",
  output_path = "data/output",
  progress_path = "data/progress",
  ref_fasta = "data/ref_trainsets/rdp_train_set_16.fa",
  ref_fasta_spp = "data/ref_trainsets/rdp_species_assignment_16.fa",
  meta_data = "data/metadata.csv",
  fwd_error = NULL,
  rev_error = NULL,
  run_filter = "Y"
)

`packages`	list of packages to load in. Defaults to `dada2`, `MicrobioUoE`, `ggplot2`, `tidyr`, `dplyr`, `phyloseq`, `DECIPHER`
`raw_path`	the path to where the raw fastq files are. Defaults to `data/raw_fastq`
`filt_path`	the path to where the filtered fastq files should be put. Defaults to `data/filtered_fastq`
`plot_path`	path to where the plots will be saved. Defaults to `plots`
`output_path`	path to where output will be saved. Defaults to `data/output`
`progress_path`	path to where progress files will be saved. Defaults to `data/progress`
`ref_fasta`	path to reference fasta file for taxonomic assignment. Defaults to `data/ref_trainsets/rdp_train_set_16.fa`
`ref_fasta_spp`	path to reference fasta file for species assignment. Defaults to `data/ref_trainsets/rdp_species_assignment_16.fa`
`meta_data`	path to metadata file. Defaults to `data/metadata.csv`
`fwd_error`	path to forward error rate if previously estimated. Ignores by default
`rev_error`	path to reverse error rate if previously estimated. Ignores by default
`run_filter`	whether or not to run the filtering step. Defaults to 'Y' for yes.

sets up the environment at the beginning of raw_read_processing.R and big_data_processing.R so that the scripts run well. Assigns all the necessary paths and loads in necessary packages and data

a bunch of paths and creates the necessary folders to make sure the environment is prepared for running the dada2 pipeline

Daniel Padfield

padpadpadpad/MicrobioUoE documentation built on April 6, 2020, 6:28 p.m.