alignPEAKS-massFlowTemplate-method: Align peaks detected in LC-MS samples using spectral...

Description Usage Arguments Details Value See Also

Description

Method aligns peaks across samples in LC-MS experiment using spectral similarity comparison. To enable alignment, peaks originating from the same chemical compound were grouped into peak-groups, via function groupPEAKS.

Usage

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## S4 method for signature 'massFlowTemplate'
alignPEAKS(object, out_dir = NULL,
  ncores = 2, cutoff = 0, write_int = FALSE)

Arguments

object

massFlowTemplate class object, created by buildTMP constructor function.

out_dir

character specifying desired directory for output.

ncores

numeric for number of parallel workers to be used. Set 1 for serial implementation. Default set to 2.

cutoff

numeric for spectra similarity score threshold, set to 0 by default.

write_int

logical specifying whether a peak table with alignment results should be saved for every sample. If TRUE, csv files will be written in the out_dir directory. Default set to FALSE

Details

Peaks are aligned across samples in their original acquisition order. Template is list of all previously detected and aligned peaks. For each peak in a sample, alignPEAKS:

Spectral similarity is measured by obtaining the cosine of the angle between two 2D vectors, representing each peak-group's m/z and intensity values.

Value

Method updates massFlowTemplate class object. Slot @tmp is updated after each round of sample alignment. Slot @data stores alignment results for each sample in the experiment. Method writes alignment results to a csv file for each sample in the experiment.

See Also

buildTMP, validPEAKS, massFlowTemplate-class


lauzikaite/massFlowR documentation built on Dec. 16, 2019, 6:01 p.m.