template for creating a metadata list for an OmicSignature R6 object
Source:R/createMetadata.R
createMetadata.Rd
updated 10/2025
Usage
createMetadata(
signature_name,
organism,
phenotype = "unknown",
assay_type,
covariates = NULL,
platform = "unknown",
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. input as a single string. e.g. "Gene KO", "Parkinson disease". Use "unknown" or NULL if not applicable.
- assay_type
required. must be one of the following: "transcriptomics", "proteomics", "metabolomics", "methylomics", "methylomics", "genetic_variations", "DNA_binding_sites", or "others". some of the common misspells, e.g. "gene", "protein" and "metab" will be changed automatically.
- covariates
optional. input covariates as a single string, and separate multiple covariates using comma, e.g. "age, gender".
- platform
optional but highly recommended. input as a single string. e.g. "transcriptomics by single-cell RNA-seq".
- direction_type
required. the direction information of the signature. "uni" or "uni-directional" if the signature is derived from one category. "bi" or "bi-directional" if the signature is derived from group A vs group B, or it contains "up" and "down" regulated features for a continuous phenotype. "categorical" if the signature is derived from comparisons between multiple groups, e.g. A vs B vs C.
- sample_type
optional but highly recommended. a cell line or tissue from BRENDA ontology.
- signature_collection
optional. the collection name that the signature belongs to.
optional. the author's name.
- year
optional. a single-length numeric value. the year when the signature was created or published.
- PMID
optional. a single-length character value. the PubMed ID if the signature is from a published article.
- keywords
optional. key words for the signature. input as a multi-length character vector, e.g. c("longevity", "perturbation", "health").
- description
optional. free text to describe the signature. input as a single-length string. the character limit (including all spaces and symbols) is 65,535.
- category_num
required when direction_type = "categorical". numeric. a number indicates how many categories or class the signature contains.
- logfc_cutoff
optional. a single-length numeric value. log fold change cutoff used to generate the signature, if applicable.
- p_value_cutoff
optional. a single-length numeric value. p value cutoff used to generate the signature, if applicable.
- adj_p_cutoff
optional. a single-length numeric value. adjusted p-value, e.g. fdr, cutoff used to generate the signature, if applicable.
- score_cutoff
optional. a single-length numeric value. score cutoff used to generate the signature, if applicable.
- cutoff_description
optional. description 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").