CombinePeaklists: Combine Peaklists from different ion modes

In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description

Combines Peaklists from positive and negative ionization modes while removing ion mode duplicates. See combine_ion_modes(), search_IonDup() for more details. For examples, see InitWorkflow() and vignettes.

Usage

CombinePeaklists(
  from.tables,
  to.table,
  method,
  peak.db,
  db.dir,
  gen.plots,
  CAMERA.pos,
  CAMERA.neg
)

Arguments

from.tables	character vector of table names to draw from databases to be combined. If gen.plots == TRUE, should be of length 2. Otherwise, only the first element will be used.
to.table	to which table should LUMA save the modified Peak.list
method	which method to use for removing ion mode duplicates. See search_IonDup for available methods.
peak.db	what database contains the Peaklists to be combined. Default is 'Peaklist_db'
db.dir	directory containing the database. Default is 'db'
gen.plots	logical indicating whether LUMA needs to generate plots to inspect ion mode duplicates. Default is to check whether this variable was assigned by a call to InitWorkflow().
CAMERA.pos	which CAMERA object to use to plot metabolite groups for positive mode. Default is to read from saved R objects by call to InitWorkflow().
CAMERA.neg	which CAMERA object to use to plot metabolite groups for negative mode. Default is to read from saved R objects by call to InitWorkflow().

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