FTAnalysisParam: Constructor for FTAnalysisParam class
In mjhelf/Mosaic: Metaboseek platform

FTAnalysisParam

R Documentation

Constructor for FTAnalysisParam class

Description

Construct a FTAnalysisParam object with parameters for use with analyzeFT()

Usage

FTAnalysisParam(
  intensities = character(),
  groups = list(),
  .files = character(),
  analyze = c("Basic analysis", "clara_cluster", "t-test", "Peak shapes",
    "Fast peak shapes", "PCA features", "PCA samples", "mzMatch", "Calculate M"),
  normalize = T,
  useNormalized = T,
  logNormalized = F,
  normalizationFactors = NULL,
  zeroReplacement = 1,
  replaceNAs = 0,
  ppm = 5,
  controlGroup = NULL,
  p.adjust.method = "fdr",
  numClusters = 2,
  mzMatchParam = list(db = "smid-db_pos.csv", ppm = 5, mzdiff = 0.001),
  workers = 1
)

Arguments

`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.
`.files`	character() with file paths to the MS data files to be used in an analysis
`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
`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
`ppm`	ppm range for peak shape analysis
`controlGroup`	control group for foldChange (part of Basic analysis) analysis (optional)
`p.adjust.method`	method to adjust p-values (see `p.adjust()`)
`numClusters`	number of clusters for clara_clusters analysis
`mzMatchParam`	list of parameters passed to mass
`workers`	number of workers to use for multithreaded analyses