template for creating a metadata list for an OmicSignature R6 object

updated 02/2024

Usage

createMetadata(
  signature_name,
  organism,
  phenotype = "unknown",
  assay_type,
  covariates = "none",
  platform = "GPLXXXXX",
  direction_type,
  sample_type = NULL,
  signature_collection = NULL,
  author = NULL,
  year = NULL,
  PMID = NULL,
  keywords = NULL,
  description = NULL,
  category_num = NULL,
  logfc_cutoff = NULL,
  p_value_cutoff = NULL,
  adj_p_cutoff = NULL,
  score_cutoff = NULL,
  cutoff_description = NULL,
  others = NULL
)

Arguments

signature_name: required. name of the signature.
organism: required. e.g. "Homo Sapiens", "Mus Musculus".
phenotype: optional but highly recommended. e.g. "Gene KO", "Parkinson disease". Use "unknown" or NULL if not applicable.
assay_type: required. e.g. "transcriptomics", "proteomics", "metabolomics", "methylomics", "methylomics", "genetic_variations", "DNA_binding_sites". some common misspell, e.g. "gene", "protein", "metab" will be changed automatically.
covariates: optional. e.g. "gender", "age".
platform: optional but highly recommended. GEO platform name. e.g. "GPL11154" is for Illumina HiSeq 2000 Homo sapiens. Use "GPLXXXXX" or NULL if not available.
direction_type: required. the direction information of the signature. "uni" or "uni-directional" if signature has only one direction or no direction infomation. "bi" or "bi-directional" if signature contains "up" and "down" regulated features. "categorical" if the signature contains more categories.
sample_type: optional but highly recommended. a cell line or tissue from BRENDA ontology.
signature_collection: optional. collection name that the signature belongs to.
author: optional. the author name.
year: optional. the year when the signature was created or published.
PMID: optional. the PubMed ID if the signature is from a published article.
keywords: optional. key words for the signature. examples are "longevity", "perturbation". "drug".
description: optional. free text to describe the signature.
category_num: required when direction_type = "categorical". numeric. indicates how many categories or class the signature contains.
logfc_cutoff: optional. log fold change cutoff used to generate the signature, if applicable.
p_value_cutoff: optional. p value cutoff used to generate the signature, if applicable.
adj_p_cutoff: optional. adjusted p-value, e.g. fdr, cutoff used to generate the signature, if applicable.
score_cutoff: optional. score cutoff used to generate the signature, if applicable.
cutoff_description: optional. discription of the cutoff, if applicable.
others: provide additional user-defined metadata fields as a list. for example, others = list("animal_strain" = "C57BL/6", "lab" = "new_lab").

Value

a metadata list to create an OmicSignature R6 object.