flag_remove: Flag and remove unwanted peaks

View source: R/flag-filter-remove.R

flag_removeR Documentation

Flag and remove unwanted peaks

Description

Filter, flag and remove unwanted peaks from xcms object (xcmsObj) of class XCMSnExp, xcmsSet or xsAnnotate. When the peaks are removed, the xcmsObj object can be regrouped (originally using xcms::group, now using xcms::groupChromPeaks). The function then checks if any blank peaks are still present and the process is repeated.

The output is a list object containing: 1) the updated xcms object, 2) the grouped peaklist and 3) the blank removed peaks

Usage

flag_remove(
  xcmsObj,
  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 = 0.017,
  bw = 5,
  out_dir = ".",
  temp_save = FALSE,
  remove_spectra_bool = TRUE,
  grp_rm_ids = NA,
  xset = NA
)

Arguments

xcmsObj

object; XCMSnExp, xcmsSet or xsAnnotate 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 (corresponds to variable 'binSize' in XCMS3)

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

bool; TRUE if flagged spectra is to be removed

grp_rm_ids

vector; vector of grouped_xcms peaks to remove (corresponds to the row from xcms::group output)

xset

object, DEPRECATED; xcmsSet object

Value

list(xset, grp_peaklist, removed_peaks)

Examples

library(xcms)
library(MSnbase)
library(magrittr)
#read in files and data
msPths <-list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE)
ms_data = readMSData(msPths, mode = 'onDisk', msLevel. = 1)

#subset the data to focus on retention times 30-90 seconds and m/z values between 100 and 200 m/z.
rtr = c(30, 90)
mzr = c(100, 200)
ms_data = ms_data %>%  filterRt(rt = rtr) %>%  filterMz(mz = mzr)

##### perform feature detection in individual files
cwp <- CentWaveParam(snthresh = 3, noise = 100, ppm = 10, peakwidth = c(3, 30))
xcmsObj <- findChromPeaks(ms_data, param = cwp)
xcmsObj@phenoData@data$class = c('blank', 'blank', 'sample', 'sample')
xcmsObj@phenoData@varMetadata = data.frame('labelDescription' = 'sampleNames', 'class')
pdp <- PeakDensityParam(sampleGroups = xcmsObj@phenoData@data$class, minFraction = 0, bw = 5, binSize = 0.017)
xcmsObj <- groupChromPeaks(xcmsObj, param = pdp)

#### flag, filter and remove peaks, returning an updated xcmsObj (XCMSnExp or xcmsSet class), grouped_peaklist (data.frame) and removed_peaks (data.frame)
fr <- flag_remove(xcmsObj)

##### load from existing data
xcmsObj = readRDS(system.file("extdata", "tests", "purityA", "10_input_filterflagremove.rds", package="msPurity"))





computational-metabolomics/msPurity documentation built on May 13, 2024, 7:36 p.m.