pmfxcms.2: pmfxcms

In cbroeckl/csu.pmf.tools: a collection of features used internally at CSU PMF for non-targeted metabolomics data processing

pmfxcms

Description

A wrapper function for XCMS using common PMF platforms.

Usage

pmfxcms.2(
  filetype.ms1 = "_01.mzML",
  filetype.ms2 = "_02.mzML",
  sequence = "seq.csv",
  delim = "-",
  ms.res = 30000,
  peak.width = c(3, 30),
  sn = 5,
  minfrac = 0.4,
  bw.pre = 3,
  bw.post = 1.2,
  n.cores = 4,
  reprocess = NULL
)

Arguments

filetype.ms1	File extension of raw data for MS level data. This extention will be scanned in all raw data files in working directory and will be added to filenames in sequence .csv file
filetype.ms2	File extension of raw data for MSe level data. If not MSe data, set to NA. This extention will be scanned in all raw data files in working directory and will be added to filenames in sequence .csv file
sequence	.csv file containing filenames (no extension) in first column, and sample name and/or factor names in remaining columns.
delim	symbol used to delimit factors in sequence file. "-" by default.
ms.res	numerical value representing mass resolution of the MS system. if NA, assumed to be quad data (low res). if numeric, used to set mass tolerances for xcms.
peak.width	numerical vector of length two giving peak width range in seconds i.e. c(3, 30)
sn	signal to noise threshold for peak detection
minfrac	minimum proportion of samples in which a feature must be present (at one MS level). i.e. 0.4 is 4 out of 10.
bw.pre	bandwidth for pre-rt correction grouping. suggested value is 3, but if there is a good deal of retention drift over the sample set a larger value should be used.
bw.post	bandwidth for post-rt correction grouping. suggested values is 1.5.
reprocess	filepath/name - should we try reprocessing an existing xcmsSet? provide file name. Will reprocess all steps after peak detection.

Details

This function uses a template file as input to guide XCMS parameter selection.

Peak detection using centwave (LC-TOF) or matchedFilter (GC-Quad), density based peak grouping, loess rt correction, regrouping, and fillPeaks.

Additionally performs unsupervised removal of ultrawide chromatgoraphic peaks and outlier detection and removal after peak detection step.

an XCMS object is returned.

Value

returns an xcms object

Author(s)

Corey Broeckling

cbroeckl/csu.pmf.tools documentation built on Jan. 26, 2024, 6:27 p.m.