flag_remove {msPurity}R Documentation

Flag and remove unwanted peaks

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)

[Package msPurity version 1.16.2 Index]