multiEIC: multiEIC

multiEICR Documentation

multiEIC

Description

Extract EICs from multiple files for multiple features.

Usage

multiEIC(
  rawdata,
  mz,
  rt,
  rnames = row.names(mz),
  byFile = F,
  XIC = F,
  getgauss = F,
  RTcorr = NULL,
  workers = 1,
  quickshapes = F,
  SN = NULL,
  scoreBy = "intmean"
)

Arguments

rawdata

a (named) list of xcmsRaw objects, e.g. generated by Metaboseek::loadRawM, OR an MSnbase OnDiskMSnExp object

mz

a data.frame with minimum (column 1) and maximum (column 2) m/z values in each row.

rt

a data.frame with minimum (column 1) and maximum (column 2) retention time values (in seconds) in each row.

rnames

names of the rows in the result matrix, typically the row.names of the feature table, or the filenames if byFile =T.

byFile

a data.frame with columns File and Group , holding file paths and group names, respectively.

XIC

deprecated

getgauss

additionally, fit a gauss curve to each EIC (time consuming), defaults to FALSE

RTcorr

if not NULL, this RTcorr object will be used to adjust retention times.

workers

number of workers for parallel processing

quickshapes

get quickshapes score instead of geegauss results

SN

when calculating peak quality with quickshapes, reject any peaks with a signal-to-noise ratio than this (intensity range within observed rt window, MAX/ MEAN INTENSITY!)

scoreBy

specify which column is used to find which EIC to use for quickshapes

Value

a list of extracted ion chromatograms that can be read by EICplot, groupPlot, EICgeneral


mjhelf/Mosaic documentation built on April 28, 2022, 11:32 a.m.