createMetadata: template for creating a metadata list for an OmicSignature R6...
In Vanessa104/devsig: Development testing

Description Usage Arguments Value

View source: R/createMetadata.R

template for creating a metadata list for an OmicSignature R6 object updated 09/2020

createMetadata(
  signature_name,
  organism,
  phenotype = "unknown",
  platform,
  direction_type,
  sample_type = NULL,
  author = NULL,
  year = NULL,
  PMID = NULL,
  keywords = NULL,
  description = NULL,
  category_num = NULL,
  logFC_cutoff = NULL,
  p_value_cutoff = NULL,
  fdr_cutoff = NULL,
  score_cutoff = NULL,
  cutoff_description = NULL,
  other = NULL
)

`signature_name`	name of the signature.
`organism`	organism. e.g. "Homo Sapiens", "Mus Musculus".
`phenotype`	the phenotype of the signature. e.g. "Akt KO", "Ketodiet", "Parkinson disease", "Unknown".
`platform`	GEO platform. e.g. "GPL11154" is for Illumina HiSeq 2000 Homo sapiens, "GPL570" is for Affymetrix Human Genome U133 Plus 2.0 Array
`direction_type`	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. "multi" or "multi-directional" if the signature contains more categories.
`sample_type`	optional but highly recommended if applicable. a cell line or tissue from BRENDA ontology, or a animal strain, e.g. "C57BL/6" for C57BL/6 mice strain.
`author`	optional. the author name if the signature is from a published article.
`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`	optional, specifically used for multi-directional signature to specify 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.
`fdr_cutoff`	optional. 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.
`other`	optional. a 'list' to specify any other user-defined metadata fields.