processSeq: Perform dada2 analysis
In guokai8/microbial: Do 16s Data Analysis and Generate Figures

processSeq

R Documentation

Perform dada2 analysis

Description

Perform dada2 analysis

Usage

processSeq(
  path = ".",
  truncLen = c(0, 0),
  trimLeft = 0,
  trimRight = 0,
  minLen = 20,
  maxLen = Inf,
  sample_info = NULL,
  train_data = "silva_nr99_v138_train_set.fa.gz",
  train_species = "silva_species_assignment_v138.fa.gz",
  outpath = NULL,
  saveobj = FALSE,
  buildtree = FALSE,
  verbose = TRUE
)

Arguments

`path`	working dir for the input reads
`truncLen`	(Optional). Default 0 (no truncation). Truncate reads after truncLen bases. Reads shorter than this are discarded.
`trimLeft`	(Optional). The number of nucleotides to remove from the start of each read.
`trimRight`	(Optional). Default 0. The number of nucleotides to remove from the end of each read. If both truncLen and trimRight are provided, truncation will be performed after trimRight is enforced.
`minLen`	(Optional). Default 20. Remove reads with length less than minLen. minLen is enforced after trimming and truncation.
`maxLen`	Optional). Default Inf (no maximum). Remove reads with length greater than maxLen. maxLen is enforced before trimming and truncation.
`sample_info`	(Optional).sample information for the sequence
`train_data`	(Required).training database
`train_species`	(Required). species database
`outpath`	(Optional).the path for the filtered reads and th out table
`saveobj`	(Optional).Default FALSE. save the phyloseq object output.
`buildtree`	build phylogenetic tree or not(default: FALSE)
`verbose`	(Optional). Default TRUE. Print verbose text output.