EvaluatePairsFromXCMSSet: EvaluatePairsFromXCMSSet.

View source: R/EvaluatePairsFromXCMSSet.R

EvaluatePairsFromXCMSSetR Documentation

EvaluatePairsFromXCMSSet.

Description

EvaluatePairsFromXCMSSet will analyze an xcmsSet result for mass pairs (mz1, mz2) with changes due to any 13C incorporation.

Usage

EvaluatePairsFromXCMSSet(
  xg = NULL,
  tp = NULL,
  gr = NULL,
  drt = 1,
  dmz = 0.025,
  mz_iso = 1.00335,
  n = 6,
  method = c("APCI", "ESI")[1],
  specific_row = NULL,
  testing = FALSE,
  silent = FALSE
)

Arguments

xg

xcmsSet object with group information.

tp

Timepoint information for all samples (obviously required, internally converted to factor).

gr

Group information for all samples, e.g. different genotypes or concentrations (optional, factor).

drt

Allowed rt deviation in time units of xcmsSet (usually seconds) to test for candidates.

dmz

Allowed mass deviation in Da.

mz_iso

Mass defect of the isotope under investigation.

n

Number of maximal incorporated carbons to test.

method

Currently APCI or ESI. If APCI, dmz will be modified depending on n (see details).

specific_row

A single row from groupval(xg) to process.

testing

Stop in function using browser() if specific_row is specified; can be a isotope number, i.e. 3 will stop at third isotope.

silent

Suppress warnings and console output if TRUE.

Details

Using 'APCI' as method assumes that (i) you analyze TMS-derivatized compounds and (ii) your MS resolution does not allow to seperate Si and C isotopes but reportes an intermediate mass as m/z. In this case you will find carbon isotopes below there expected masses, i.e. M+1 would be 1.001mDa apart from M+0 instead of 1.003. The effect is increased with isotope number, i.e. M+6 will be ~20mDa below the expected value. Hence, selecting method 'APCI' will combine your selected dmz with a allowed deviation due to Si-isotope caused mass shifts. Use 'ESI' if you are not sure if this effect takes place in your settings.

Value

A dataframe with all observable pairs within the provided xcmsSet peak list including mean group intensities and P values.

Examples

# Please use examples from previous versions as xcms (and xcms objects) are
# no longer supported during CRAN checks leading to package rejection
# if included (and I do not know a work around).
## Not run: 
load(xcms_cand)
head(xcms_cand[order(xcms_cand$P), ])

## End(Not run)


HiResTEC documentation built on March 7, 2023, 5:47 p.m.