massFlowTemplate-class: massFlowTemplate, a class for sample alignment and annotation
In lauzikaite/massFlowR: LC-MS Data Pre-Processing

Description Usage Arguments Details Value Slots See Also

This class enables the alignment of LC-MS samples. It takes files containing groups of structurally related peaks, generated by groupPEAKS function, and aligns them in their original sample acquisition order. It validates peak groups obtained during alignment by correlating peak intensities in all samples. Finally, it fills in missing peak intensity values using raw data.

validmassFlowTemplate(object, realtime = FALSE)

## S4 method for signature 'massFlowTemplate'
show(object)

## S4 method for signature 'massFlowTemplate'
checkNEXT(object)

`object`	`massFlowTemplate` class object
`realtime`	`logical`

massFlowTemplate object stores sample alignment data.

Slot @tmp is the template, listing information for every detected peak, such as the m/z, rt, into values and the assigned peak-group.
Template is first built using the first datafile in the study. To initiate template built, constructor function buildTMP must be called, providing a "filepath" to the csv file with the details on the study samples.
Template is updated with every round of sample alignment. Alignment results are stored in slot @data for each sample separately.

Method returns filename to be processed next.

filepath: character specifying the absolute path to a csv file with study sample names and their acquisition (run) order.
samples: data.frame storing study sample names and their acquisition order.
tmp: data.frame storing sample alignment and annotation template.
data: list containg annotated and aligned peak tables for the already processed samples.
params: list containg alignment and annotation parameters.
valid: data.frame storing validated sample alignment template with peakids and corresponding Pseudo Chemical Spectra id.
peaks: list containing peak intergration values for every peak (NA if peak was not detected), listead peak-wise.
values: list containing peak intergration values for every sample (NA if peak was not detected), listed sample-wise.
history: list containg names of methods that have already been applied to the object.