FormatForMetaboAnalystR: Formatting of metabolite data for MetaboAnalystR.

In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description

This function initializes objects that will hold the metabolite data, formats peak intensity data into one of the formats acceptable by MetaboAnalystR, and sets the metabolite data object. For examples, see InitWorkflow() and vignettes.

Usage

FormatForMetaboAnalystR(
  from.table,
  to.csv,
  data.type = "pktable",
  anal.type = "stat",
  paired = FALSE,
  peak.db,
  db.dir
)

Arguments

from.table	from which table should LUMA read the Peaklist
to.csv	to what filename (excluding .csv extension) should LUMA save the formatted Peaklist
data.type	What type of data will be generated. See usage and format_MetabolomicData for options.
anal.type	character Indicates the analysis module the data will be used for. See usage and documentation for MetaboAnalystR::InitDataObjects() for options.
paired	logical Indicate if the data is paired or not. Default is FALSE
peak.db	what database contains the Peaklists to be combined. Default is "Peaklist_db".
db.dir	directory containing the database. Default is "db".

Value

mSetObj

USEPA/LUMA documentation built on Aug. 29, 2020, 1:40 p.m.