md_postprocess: Postprocess metadata prepared using md_preprocess()

In metamaden/rmpipeline: Process DNAm array IDATs into database files

Postprocess metadata prepared using md_preprocess()

Description

Perform postprocessing of previously prepreocessed sample metadata. This produces the new harmonized variables (specified by arg mdpost.vl), where harmonization means terms are mapped, lowercase, and "_" separated. Variable entries can include multiple terms separated by ";". The args mdpre.vl and mdpost.vl specify the various variable titles in the preprocess and postprocess dataset. The vars disease.search.vars, tissue.search.vars, and storage.info.vars specify the mdpre variables to search for disease, tissue, and storage info mappings.

Usage

md_postprocess(
  ts,
  mdpre,
  mdpost.fname = "md_postprocess",
  md.dpath = file.path("recount-methylation-files", "metadata"),
  mdpre.vl = list(study_id = "gse", sample_id = "gsm", sample_title = "gsm_title",
    disease = "disease_state", sample_type = "sample_type", sex = "sex", info = "info",
    age = "age", age_temp = "age_temp"),
  mdpost.vl = list(tissue = "tissue", disease = "disease", age = "age", sex = "sex",
    storageinfo = "storageinfo"),
  disease.search.vars = c("sample_title", "disease"),
  tissue.search.vars = c("sample_type", "sample_title"),
  storage.info.vars = c("sample_type", "sample_title", "info"),
  verbose = TRUE
)

Arguments

ts	The timestamp for this run.
mdpre	The matrix containing preprocessed metadata (returned from md_preprocess()).
mdpost.fname	Filename for newly mapped postprocessed metadata.
md.dpath	Path to the directory containing the preprocessed metadata matrix, where newly postprocessed metadata will be stored.
mdpre.vl	List mapping term categories (names) to column names in the mdpre preprocessed metadata matrix.
mdpost.vl	List mapping term categories (names) to column names in the mdpost postprocessed metadata matrix to be generated.
disease.search.vars	Term categories to search in preprocessed metadata for the disease term mappings
tissue.search.vars	Term categories in preprocessed metadata to search for tissue term mappings.
storage.info.vars	Term categories in preprocessed metadata to search for storage information term mappings.
verbose	Whether to show status messages (TRUE).

Value

Postprocessed metadata table.

See Also

md_preprocess()

metamaden/rmpipeline documentation built on Jan. 12, 2023, 3:20 p.m.