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new_reference

Source: R/new_reference.R
new_reference.Rd

Create a resource reference for your strollur object to aid in reproducibility.

Usage

new_reference(
  name,
  vendor = "",
  version = "",
  usage = "",
  note = "",
  documentation_url = "",
  method_url = "",
  parameter = "",
  citation = ""
)

Arguments

name,

a string containing the name of the resource used. For example: 'silva.bacteria.fasta' or 'R package phylotypr'.

vendor

a string containing name of entity that created original resource. example: "Silva" or "Schloss Lab - University of Michigan"

version,

a string containing the version of the reference resource. For example: '1.38.1' or '0.1.1'. Default = "".

usage,

a string containing the usage of the resource reference in your analysis. For example: 'alignment of sequences' or 'classification of sequences'. Default = "".

note,

a string containing additional notes about the resource reference in your analysis. For example: 'alignment reference trimmed to V4 region' or 'classification of sequences using Bayesian method'. Default = "".

documentation_url,

a string containing a web address where the reference may be downloaded or documentation may be found. Default = "".

method_url,

a string containing any publications describing the methods used by the resource reference. For example: 'doi:10.1128/mra.01144-24'. Default = "".

parameter,

a string containing the any specific parameters used by the resource. For example: 'kmer_size = 8, num_bootstraps = 100, min_confidence = 80' Default = "".

citation,

a string containing the citation information for the resource reference. For example: "citation_key = "doi:10.1128/AEM.00062-07", author = "Qiong Wang and George M. Garrity and James M. Tiedje and James R. Cole", title = "Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy", journal = "Applied and Environmental Microbiology", volume = "73", number = "16", pages = "5261-5267", year = "2007", doi = "10.1128/AEM.00062-07"". Default = "".

Value

a list

Examples


silva_resource <- new_reference(
  vendor = "SILVA", name =
    "silva.bacteria.fasta", version = "1.38.1",
  usage = "alignment of sequences",
  note = "alignment reference trimmed to V4 region", documentation_url =
    "https://mothur.org/wiki/silva_reference_files/", method_url =
    "https://mothur.org/blog/2024/SILVA-v138_2-reference-files/"
)

phylotypr_resource <- new_reference(
  vendor = "Schloss Lab - University of
Michigan", name = "R phylotypr package", version = "0.1.1", usage =
    "classification of sequences",
  note = "classification using Bayesian method",
  parameter = "kmer_size = 8, num_bootstraps = 100, min_confidence = 80",
  documentation_url = "https://mothur.org/phylotypr/", method_url =
    "doi:10.1128/mra.01144-24",
  citation = "@article{doi:10.1128/AEM.00062-07,
author = {Qiong Wang and George M. Garrity and James M. Tiedje and James R.
Cole}, title = {Naïve Bayesian Classifier for Rapid Assignment of rRNA
Sequences into the New Bacterial Taxonomy}, journal = {Applied and
Environmental Microbiology}, volume = {73}, number = {16}, pages =
{5261-5267}, year = {2007}, doi = {10.1128/AEM.00062-07}, URL =
{https://journals.asm.org/doi/abs/10.1128/aem.00062-07}, eprint =
{https://journals.asm.org/doi/pdf/10.1128/aem.00062-07}}"
)