isotopic_pattern: Extract experimental isotopic patterns from a table of MS...

In RuggeroFerrazza/IsotopicLabelling: A package for the analysis of MS isotopic patterns in labelling experiments

Description

Function that extracts the experimental isotopic patterns of a specified compound from a data frame containing MS peak intensities or areas.

Usage

isotopic_pattern(peak_table, info, mass_shift, RT, RT_shift, chrom_width)

Arguments

peak_table	Data frame of experimental MS peak intensities or areas (one column for each sample), with the first two columns representing m/z and retention times of the peaks
info	Named list containing isotopic information, output of the isotopic_information function
mass_shift	Maximum difference between theoretical and experimental mass. In other words, the expected mass accuracy
RT	Expected retention time of the compound of interest
RT_shift	Maximum difference between expected and experimental retention time of the peaks
chrom_width	An estimate of the chromatographic peak width

Details

The table can be obtained from an xcmsSet object (output of the xcms R package) through the table_xcms function.

Value

A matrix of extracted experimental isotopic patterns (one column for each sample), with the first two columns representing the exact m/z and the retention times of the peaks

Author(s)

Ruggero Ferrazza

See Also

table_xcms , isotopic_information

Examples

## Not run: 
experimental_patterns <- isotopic_pattern(peak_table, info, mass_shift=0.05, 
RT=285, RT_shift=20, chrom_width=7)

## End(Not run)

RuggeroFerrazza/IsotopicLabelling documentation built on May 9, 2019, 10:36 a.m.