Skip to contents

Default parameters

Source: R/phylotaR.R
parameters.Rd

Returns a parameter list with default parameter values.

Usage

parameters(
  wd = ".",
  txid = character(),
  mkblstdb = "",
  blstn = "",
  v = FALSE,
  ncps = 1,
  mxnds = 1e+05,
  mdlthrs = 3000,
  mnsql = 250,
  mxsql = 2000,
  mxrtry = 100,
  mxsqs = 50000,
  mxevl = 1e-10,
  mncvrg = 51,
  btchsz = 100,
  db_only = FALSE,
  outsider = FALSE,
  srch_trm = paste0("NOT predicted[TI] ", "NOT \"whole genome shotgun\"[TI] ",
    "NOT unverified[TI] ", "NOT \"synthetic construct\"[Organism] ",
    "NOT refseq[filter] NOT TSA[Keyword]"),
  date = Sys.Date()
)

Arguments

wd

The working directory where all output files are saved.

txid

Taxonomic group of interest, allows vectors.

mkblstdb

File path to makeblastdb

blstn

File path to blastn

v

Print progress statements to console? Statements will always be printed to log.txt.

ncps

The number of threads to use in the local-alignment search tool.

mxnds

The maximum number of nodes descending from a taxonomic group. If there are more than this number, nodes at the lower taxonomic level are analysed.

mdlthrs

'Model organism threshold'. Taxa with more sequences than this number will be considered model organisms and a random mdlthrs subset of their sequences will be downloaded.

mnsql

The minimum length of sequence in nucleotide base pairs to download.

mxsql

The maximum length of sequence in nucleotide base pairs to download. Any longer sequences will be ignored.

mxrtry

The maximum number of attempts to make when downloading.

mxsqs

The maximum number of sequences to BLAST in all-vs-all searches. If there are more sequences for a node, BLAST is performed at the lower taxonomic level.

mxevl

The maximum E-value for a successful BLAST.

mncvrg

The maximum percentile coverage defining an overlapping BLAST hit. Sequences with BLAST matches with lower values are not considered orthologous.

btchsz

Batch size when querying NCBI

db_only

Take sequences only from restez library? TRUE/FALSE. If TRUE, internet is still required (for taxonomic look-up) and a restez will need to be set up.

outsider

Use om..blast? TRUE/FALSE. If TRUE, a module for running blastn will be installed and all BLAST commands will be run through it. outsider package is required.

srch_trm

Sequence NCBI search term modifier. Use this parameter to change the default search term options. Default: avoid predicted, WGS, unverified, synthetic, RefSeq and Transcriptome Shotgun Assembly sequences.

date

Date when pipeline was initiated

Value

list

Details

This function is NOT used to change the parameters in a folder. Use parameters_reset() instead. The purpose of this function is to describe the paramaters and present their default values.