InitWorkflow: Constructor module to initiate LUMA Workflow

In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description

All LUMA workflows must start with this module Creates the first Peaklist and sets up storing and passing Peaklists and ancillary data between modules. For examples, see InitWorkflow() and vignettes.

Usage

InitWorkflow(
  ion.id,
  db.dir,
  use.CAMERA,
  use.XCMS,
  CAMERA.obj,
  XCMS.obj,
  graph.method,
  QC.id,
  ion.mode,
  mytable,
  calc.minfrac,
  multiple
)

Arguments

ion.id	character vector specifying identifier in mzdata filenames designating positive or negative ionization or both. Must be a (case-insensitive) abbreviation of the ionization mode name. Positive identifier must come first. Default is c("Pos","Neg").
db.dir	character name of subdirectory to store databases. Default is "db"
use.CAMERA	logical indicating whether to use existing CAMERA object in global environment. Default is to look for CAMERA objects saved by previous calls to this function and run CAMERA if missing.
use.XCMS	logical indicating whether to use existing XCMS object in global environment. Default is to look for XCMS objects saved by previous calls to this function and run XCMS if missing.
CAMERA.obj	which CAMERA object to use to initialize LUMA workflow. Only relevant if use.CAMERA == TRUE.
XCMS.obj	which XCMS object to use to initialize LUMA workflow. Only relevant if use.XCMS == TRUE.
graph.method	graphing method to use for CAMERA. Default is "lpc". See CAMERA documentation for details.
QC.id	character vector specifying identifier in filename designating a Pooled QC sample. Only the first value will be used. Default is "Pooled_QC_"
ion.mode	which ion mode(s) will be processed for this data. Must be one or both of c("Positive","Negative"). Default is both.
mytable	character name of the first Peaklist table in the database. Default is "From_CAMERA".
calc.minfrac	logical should LUMA calculate the minimum fraction values for the initial Peaklist. Default is TRUE.
multiple	logical should multiple fields be allowed in dialog boxes. Default is FALSE.

Value

global variables and Peaklist in database are returned

Examples

## Not run: 
library(LUMA)
if(require(lcmsfishdata, quietly = TRUE)) {
  db.dir <- system.file("extdata", package = "lcmsfishdata")
  InitWorkflow(db.dir = db.dir)
  AnnotatePeaklist(from.table = "From_CAMERA", to.table = "Annotated")
  FinalWorkflow(peak_db = peak_db, lib_db = lib_db)
  }

## End(Not run)

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