processSeq {microbial}

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.

Value

list include count table, summary table, taxonomy information and phyloseq object

Author(s)

Kai Guo