alignPEAKS-massFlowTemplate-method: Align peaks detected in LC-MS samples using spectral...
In lauzikaite/massFlowR: LC-MS Data Pre-Processing

Description Usage Arguments Details Value See Also

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.

1 2	## S4 method for signature 'massFlowTemplate' alignPEAKS(object, out_dir = NULL, ncores = 2, write_int = FALSE)

`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.
`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

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:

Finds all template peaks within a m/z and rt window.
Identifies the true match by comparing the spectral similarity between the peak-group of the peak-of-interest and all matching template's peak-groups.
Merges the selected template's peak-group with the peak-group of the peak-of-interest.
Updates template's m/z and rt values for the matching peaks across the template and the sample.

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.

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.

buildTMP, validPEAKS, massFlowTemplate-class

lauzikaite/massFlowR documentation built on April 29, 2020, 9:45 a.m.