massFlowTemplate-class: massFlowTemplate, a class for sample alignment and annotation

Description Usage Arguments Details Value Slots See Also

Description

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.

Usage

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validmassFlowTemplate(object, realtime = FALSE)

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

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

Arguments

object

massFlowTemplate class object

realtime

logical

Details

massFlowTemplate object stores sample alignment data.

Value

Method returns filename to be processed next.

Slots

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.

See Also

buildTMP, alignPEAKS, validPEAKS


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