get_replicates: Get likely sample replicates

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

Get likely sample replicates

Description

Use inferred genotypes to predict sample replicates by study. This function uses the genotype prediction methods in the ewastools package to predict likely sample replicates for each included study.

Usage

get_replicates(
  ts,
  rg.fname,
  athresh = 0.1,
  md = NULL,
  md.dname = "metadata",
  comp.dname = "compilations",
  files.dname = "recount-methylation-files",
  verbose = TRUE
)

Arguments

ts	Timestamp for the metadata output (integer or character).
athresh	Similarity threshold for replicate identification (0.1).
md	Preprocessed metadata, rsheet, or other table containing columns "gsm" and "gse". If NULL, attempt to find mdpre at md.dname (NULL).
md.dname	Name of metadata dir ("metadata"), contained at files.dname.
comp.dname	Name of compilations dir ("compilations"), contained at files.dname.
files.dname	Name of files dir for the instance ("recount-methylation-files").
verbose	Whether to show status messages (TRUE).
rgset	An RGChannelSet object.

Value

NULL, stores a table of replicate information.

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