FTAnalysisParam-class: Parameter class for Feature Table analysis

In mjhelf/Mosaic: Metaboseek platform

Parameter class for Feature Table analysis

Description

Objects of this class hold parameters for feature table analysis, to be used with analyzeFT()

Details

FTAnalysisParam

Slots

intensities

the intensity column names, before normalization (without __norm suffix), will be automatically renamed if useNormalized.

groups

named list of non-normalized intensity columns listed by group (as supplied by $anagroupnames of MseekFT objects), will be automatically renamed if useNormalized.

analyze

character vector to select the analyses to be run: "Basic analysis", "clara_cluster", "t-test", "Peak shapes"

normalize

normalze intensity columns

useNormalized

use normalized values for analyses; will trigger normalize if there is no normalized data available for all selected intensity columns

logNormalized

if TRUE, applies a log10 to intensity values after normalization

.files

character() with file paths to the MS data files to be used in an analysis

ppm

ppm range for peak shape analysis

controlGroup

control group for foldChange (part of Basic analysis) analysis (optional)

numClusters

number of clusters for clara_clusters analysis

mzMatchParam

list of parameters passed to mass

workers

number of workers to use for multithreaded analyses

normalizationFactors

normalizationFactors vector with factors to apply to each column for normalization.

zeroReplacement

value to replace zeros with

replaceNAs

Numeric value to replace NA values with

p.adjust.method

method to adjust p-values (see p.adjust())

mjhelf/Mosaic documentation built on April 28, 2022, 11:32 a.m.