flag_remove: Flag and remove unwanted peaks

In msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Description

On an xcmsSet object, filter flag and remove unwanted peaks. When the peaks are removed, the the xcmsSet object can be regrouped using xcms::group. The function then checks if any blank peaks are still present and the process is repeated.

The output is a list of the updated xcmsSet object, grouped peaklist and the blank removed peaks

Usage

flag_remove(
  xset,
  pol = NA,
  rsd_i_blank = NA,
  minfrac_blank = 0.5,
  rsd_rt_blank = NA,
  ithres_blank = NA,
  s2b = 10,
  ref.class = "blank",
  egauss_thr = NA,
  rsd_i_sample = NA,
  minfrac_sample = 0.7,
  rsd_rt_sample = NA,
  ithres_sample = NA,
  minfrac_xcms = 0.7,
  mzwid = 0.025,
  bw = 5,
  out_dir = ".",
  temp_save = FALSE,
  remove_spectra = TRUE,
  grp_rm_ids = NA
)

Arguments

xset	object; xcmsSet object
pol	str; polarity (just used for naming purpose for files being saved) [positive, negative, NA]
rsd_i_blank	numeric; RSD threshold for the blank
minfrac_blank	numeric; minimum fraction of files for features needed for the blank
rsd_rt_blank	numeric; RSD threshold for the RT of the blank
ithres_blank	numeric; Intensity threshold for the blank
s2b	numeric; fold change (sample/blank) needed for sample peak to be allowed. e.g. if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank = 10. 1000/10 = 100 so sample has fold change higher than the threshold and the peak is not considered a blank
ref.class	str; A string representing the class that will be used for the blank.
egauss_thr	numeric; Threshold for filtering out non gaussian shaped peaks. Note this only works if the verbose option was set for XCMS;
rsd_i_sample	numeric; RSD threshold for the sample
minfrac_sample	numeric; minimum fraction of files for features needed for the sample
rsd_rt_sample	numeric; RSD threshold for the RT of the sample
ithres_sample	numeric; Intensity threshold for the sample
minfrac_xcms	numeric; minfrac for xcms grouping
mzwid	numeric; xcms grouping parameter
bw	numeric; xcms grouping parameter
out_dir	str; out directory
temp_save	boolean; Assign True if files for each step saved (for testing purpsoses)
remove_spectra	bool; TRUE if flagged spectra is to be removed
grp_rm_ids	vector; vector of grouped_xcms peaks to remove (coresponds to the row from xcms::group output)

Value

list(xset, grp_peaklist, removed_peaks)

Examples

msPths <- list.files(system.file("extdata", "lcms", "mzML",
                     package="msPurityData"), full.names = TRUE)
xset <- xcms::xcmsSet(msPths)
xset@phenoData[,1] <- c('blank', 'blank', 'sample', 'sample')
xset <- xcms::group(xset)
fr = flag_remove(xset)

msPurity documentation built on Jan. 14, 2021, 2:44 a.m.