multiEIC {Mosaic}R Documentation

multiEIC

Description

Extract EICs from multiple files for multiple features.

Usage

multiEIC(rawdata = rawcoll, mz = data.frame(mzmin = pcame_mini$mzmin, mzmax
  = pcame_mini$mzmax), rt = data.frame(rtmin = pcame_mini$rt - 5, rtmax =
  pcame_mini$rt + 5), rnames = row.names(pcame_mini), byFile = F, XIC = F,
  getgauss = F, RTcorr = NULL)

Arguments

rawdata

a (named) list of xcmsRaw objects, e.g. generated by Mosaic::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.

[Package Mosaic version 0.7.0 Index]