metfile_init: function to initiate a metadata file from dada2 db file

In OxfordCMS/OCMSutility: Utility functions for OCMS

function to initiate a metadata file from dada2 db file

Description

metfile_init

Usage

metfile_init(
  db_file,
  out_dir = NULL,
  ref_table = NULL,
  id_orient = "col",
  dummy = NULL
)

Arguments

db_file	rsqlite database file
out_dir	output directory. default NULL (no output written to file)
ref_table	= name of table in database from which sampleID are generated. default NULL. when NULL assumes table is merged_abundance_id which is the count table produced from the ocms_16s dada2 pipeline
id_orient	= indicates orientation of sample IDs. default 'col' indicates samples are in columns. 'row' indicates samples are in rows and sample IDs are the rownames
dummy	= default NULL. when string supplied, adds a dummy column of NAs with the string as the column name.

Value

dataframe of metadata

OxfordCMS/OCMSutility documentation built on Feb. 27, 2025, 8:19 p.m.