View source: R/EvaluatePairsFromXCMSSet.R
EvaluatePairsFromXCMSSet | R Documentation |
EvaluatePairsFromXCMSSet
will analyze an xcmsSet result for mass pairs (mz1, mz2) with changes due to any 13C incorporation.
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 )
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. |
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.
A dataframe with all observable pairs within the provided xcmsSet peak list including mean group intensities and P values.
# 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)
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