StdMatchR: Standards Locater

Description Usage Arguments Value Author(s)

Description

This function searches for XCMS objects (peaks, groups) that match with the provided standards (optionally with isotopic profiles).

Usage

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StdMatchR(Standards.mz, Standards.RT, Data, Standards.ratios = NULL,
  max.ppm = NULL, max.mz = NULL, max.RT.narrow = NULL,
  max.RT.wide = NULL, accept.ppm.diff = NULL)

Arguments

Standards.mz

A vector (single standards) or matrix (isotopic profiles) with the standards.

Standards.RT

A vector with the RT values

Data

This can be either a) a matrix with 2 or 3* columns (mz, RT, Intensity*) without missing values, b) an xcmsSet object post grouping (the groups are features, intensity ratio's can be checked) or c) an XCMS@groups matrix object (if only this is supplied there will be no intensity ratio check). Note that an XCMS@peaks object is also supported but the function only returns 1 match per standard (the closest one, or the first of a number of equally close ones)

Standards.ratios

Optional matrix. Matrix with the intensity ratio's

max.ppm

maximal ppm distance

max.mz

maximal mz distance (not necessary if ppm supplied)

max.RT.narrow

preferred maximal RT distance

max.RT.wide

extended RT search area. A peak is only accepted here when the improvement in ppm difference is at least accept.ppm.diff

accept.ppm.diff

The improvement in ppm difference a peak in the wider RT area has to have for it to be accepted

Value

A list with 3 vector/matrix entries (the same size as the supplied vector/matrix with standards). The first are the matched peaks/groups. The second the ppm differences. The third the RT differences.

Author(s)

Charlie Beirnaert, charlie.beirnaert@uantwerpen.be


Beirnaert/MetaboMeeseeks documentation built on May 20, 2019, 11:09 a.m.