import_msdial_data: Import all data generated by MSDial.

In eMetaboHUB/MS-CleanR: Cleans MS Data for Easier Analyses

Import all data generated by MSDial.

Description

Import all data generated by MSDial.

Usage

import_msdial_data(
  filter_blk,
  filter_blk_threshold,
  filter_mz,
  filter_rsd,
  filter_rsd_threshold,
  filter_blk_ghost_peaks,
  filter_rmd,
  filter_rmd_range,
  threshold_mz
)

Arguments

filter_blk	A boolean indicating whether or not to delete rows with too much noise.
filter_blk_threshold	A numerical threshold for noise filtering: rows with ratio mean(blank columns)/mean(qc columns) >= filter_blk are deleted (if there are no QC columns in the sample, the mean of standard columns is used, or the mean of all non-blank samples if needed).
filter_mz	A boolean indicating whether or not to delete rows with masses ending in .8 or .9 (masses not found in natural products).
filter_rsd	A boolean indicating whether or not to delete rows with too much relative standard deviation in each class.
filter_rsd_threshold	A numerical threshold for relative standard deviation filtering: rows with relative standard deviation >= filter_rsd_threshold in each class are deleted. Only used if filter_rsd is TRUE.
filter_blk_ghost_peaks	A boolean indicating whether or not to delete blank ghost peaks (only used if filter_blk is TRUE, see publication for more information).
filter_rmd	A boolean indicating whether or not to delete rows with a Relative Mass Defect outside of the range provided in filter_rmd_range.
filter_rmd_range	A range of 2 integers indicating the acceptable Relative Mass Defects in ppm (only used if filter_rmd is TRUE).
threshold_mz	A numerical value indicating the mass tolerance in Dalton for the detection of adducts and neutral losses.

Value

A list of 4 data.frames: peak_data contains the main data about detected peaks in positive and negative modes, links contains MSDial links between peaks, detected_adducts contains the probabilities of detection of adducts based on MSDial information., samples contains samples information (names, classes, column names).

eMetaboHUB/MS-CleanR documentation built on Jan. 3, 2024, 8:55 p.m.