ProfileCleanUp {TargetSearch}R Documentation

Reduce redundancy of the profile

Description

This function reduces/removes redundancy in a profile.

Usage

ProfileCleanUp(Profile, timeSplit = 500, r_thres = 0.95)

Arguments

Profile A tsProfile object. See Profile.
timeSplit A RI window.
r_thres A correlation threshold.

Details

Metabolites that are inside a timeSplit window will be correlated to see whether the metabolites are the same or not, by using r_thres as a cutoff. If so, the intensities and RI will be averaged and the metabolite with more correlating masses will be suggested.

Value

A tsProfile object with a non-redundant profile of the masses that were searched and correlated, and intensity and RI matrices of the correlating masses.

slot "Info" A data frame with a profile of all masses that correlate and the metabolites that correlate in a timeSplit window.
slot "Intensity" A matrix with the averaged intensities of the correlating masses.
slot "RI" A matrix with the averaged RI of the correlating masses.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

See Also

Profile, tsProfile

Examples

# load example data
require(TargetSearchData)
data(TargetSearchData)

# here we use the metabProfile previously calculated and return a "cleaned" profile.
metabProfile.clean <- ProfileCleanUp(metabProfile, timeSplit = 500,
                      r_thres = 0.95) 

# Different cutoffs could be specified
metabProfile.clean <- ProfileCleanUp(metabProfile, timeSplit = 1000,
                      r_thres = 0.9) 


[Package TargetSearch version 1.0.0 Index]