combinexsAnnos: Check CAMERA ion species annotation due to matching with...
In CAMERA: Collection of annotation related methods for mass spectrometry data

Description Usage Arguments Details Value Author(s) Examples

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.

1	combinexsAnnos(xsa.pos, xsa.neg, pos=TRUE, tol=2, ruleset=NULL)

`xsa.pos`	xsAnnotate object with positive ion mode
`xsa.neg`	xsAnnotate object with neagtive ion mode
`pos`	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

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!

Returns a (normal) CAMERA peaklist with a additional column neg. Mode or pos. Mode, where matching peaks from the opposite mode are noted.

Carsten Kuhl <ckuhl@ipb-halle.de>

 ## 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)