findLabels: findLabels

In mjhelf/Mosaic: Metaboseek platform

findLabels

Description

find labeled compounds in complist which correspond to unlabeled compounds in reflist

Usage

findLabels(
  reflist,
  complist,
  ref_intensityCols,
  comp_intensityCols,
  labelmz = 2 * 1.00335,
  pktolerance = 20,
  rtdiff = 10,
  ppm_compare = 5,
  ifoldS1 = 10,
  ifoldS2 = 5,
  rawdata = NULL,
  ppm_extract = 5,
  rtw_extract = 5
)

Arguments

reflist	data.frame with molecular features and columns mz, rt, rtmin, rtmax
complist	data.frame with molecular features and columns mz, rt, rtmin, rtmax
ref_intensityCols	intensity column names in reflist
comp_intensityCols	intensity column names in complist
labelmz	expected m/z difference between reference and labeled compounds
pktolerance	maximum fold difference in retention time peak width between matched peaks
rtdiff	maximum retention time difference (same unit as rt columns in reflist and complist, typically seconds)
ppm_compare	ppm m/z tolerance for feature list comparison
ifoldS1	min. fold Iso1/Iso2 in unlabeled
ifoldS2	max. fold Iso1/Iso2 in labeled
rawdata	list of xcmsRaw objects. Item names must be contained in column names
ppm_extract	ppm m/z tolerance for EIC extraction
rtw_extract	retention time window for EIC extraction (seconds, will be applied +/- the expected rt)

Value

a data.frame based on reflist, filtered for features with matches in complist and information on a single match (best rt match).

Examples

## Not run: 
MseekExamplePreload(data = TRUE, tables = TRUE)
findLabelsResults <- findLabels(reflist = tab2$df[,!colnames(tab2$df) %in% c(tab2$intensities, paste0(tab2$intensities,"__norm"))], #remove intensity columns to have them replaced with new ones from rawdata
                                complist = tab2$df[,!colnames(tab2$df) %in% c(tab2$intensities, paste0(tab2$intensities,"__norm"))],
                                ref_intensityCols = tab2$intensities[1:3],
                                comp_intensityCols = tab2$intensities[4:7],
                                labelmz = 2*1.00335,
                                ifoldS1 = 10,
                                ifoldS2 = 10000,
                                rawdata = MSD$data)
 
## End(Not run)
 

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