combinexsAnnos: Check CAMERA ion species annotation due to matching with opposite ion mode
Description
This function check annoations of ion species with the help of a sample from opposite ion mode.
As first step it searches for pseudospectra from the positive and the negative sample
within a retention time window. For every result the m/z differences between both samples
are matched against specific rules, which are combinations from pos. and neg. ion species.
As example M+H and M-H with a m/z difference of 2.014552. If two ions matches such a difference,
the ion annotations are changed (previous annotation is wrong), confirmed or added.
Returns the peaklist from one ion mode with recalculated annotations.
If TRUE the peaklist from the positive mode is returned,
if FALSE the negative
tol
Retention time window in seconds
ruleset
Matrix of matching rules, see example
Value
Returns a (normal) CAMERA peaklist with a additional column neg. Mode or pos. Mode,
where matching peaks from the opposite mode are noted.
Details
Both xsAnnotate object should be full processed (grouping and annotation).
Without previous annotation the resulting peaklist only includes annotation
with matches peaks from both mode according to the rule(s). With ruleset=NULL
the function only looks for M+H/M-H pairs.
The ruleset is a two column matrix with includes rule indices from the rule table
of both xsAnnotate objects.
ruleset <- cbind(1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset
and xsa.neg@ruleset is M+H respectively M-H.
Only rules with identical charge can be combined!
## Not run: # #Searches for M+H/M-H combinations within a retention time window of 2 seconds# peaklist.pos <- combinexsAnnos(xsa.pos, xsa.neg, tol=2)# ## End(Not run)