Xcms.combinexsAnnos

Description

What it does?

This function check annotations 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 reten- tion 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.

Details

Both xsAnnotate object should be full processed (grouping and annotation). Without previous anno- tation 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. A ruleset (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!

Workflow position

Upstream tools

Downstream tools

The output file xset.annotateDiffreport.variableMetadata.tsv is a tabular file. You can continue your analysis using it in the following tools:

Batch_correction

Filters

Univariate

Multivariate PCA, PLS and OPLS

Place of CAMERA.combinexsannot after XCMS part of the metabolomic workflow

General schema of the metabolomic workflow

Input files

Output files

xset.combinexsAnnos.variableMetadata.tsv

A tabular file which is similar to the diffreport result , within additional columns containing the annotation results.

For each metabolite (row) :

the value of the intensity in each sample, fold, tstat, pvalue, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct, pcgroup and neg (or pos). Mode

xset.combinexsAnnos.Rdata

Rdata file, that be used outside Galaxy in R.

Working example

Output files

Example of an xset.combinexsAnnos.variableMetadata.tsv output: