multiEIC: multiEIC
In mjhelf/Mosaic: Metaboseek platform

multiEIC

R 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