getRGTVValues: Calculation of values used for a Retention time correction...

In rietho/IPO: Automated Optimization of XCMS Data Processing parameters

Calculation of values used for a Retention time correction and Grouping Target Value (RGTV)

Description

This function calculates the Retention time Correction Score (RCS) of all features within an xcmsSet-object. Also features having exactly one peak from each sample are defined as 'good groups', all others a 'bad groups'.

Usage

getRGTVValues(xset, exp_index = 1, retcor_penalty = 1)

Arguments

xset	xcmsSet object
exp_index	Experiment-id of the experiment within a Design of Experiments
retcor_penalty	Penalty if an error occured with the used retention time correction parameters

Details

This function calculates the Retention time Correction Score (RCS) of all features within an xcmsSet-object. Also features having exactly one peak from each sample are defined as 'good groups', all others a 'bad groups' which leads to a Grouping Score (GS) by calculating 'good groups'^2/'bad groups'.

Value

a list containing the items exp_index, good_groups, bad_groups, GS and RCS.

Author(s)

Gunnar Libiseller

Examples

  mtbls2files <- list.files(paste(find.package("mtbls2"), "/mzML", sep=""), 
                            full.names=TRUE)
  xset <- xcmsSet(mtbls2files[1:2], method="centWave", peakwidth=(c(12, 30)), 
                  ppm=30, noise=10000)
  xset <- retcor(xset, method="obiwarp")
  xset <- group(xset)
  getRGTVValues(xset)

rietho/IPO documentation built on Dec. 6, 2022, 8:17 a.m.