analyzeTable: analyzeTable

In mjhelf/Mosaic: Metaboseek platform

analyzeTable

Description

Run a series of analyses on a feature table data.frame

Usage

analyzeTable(
  df,
  intensities,
  groups,
  analyze = c("Basic analysis", "clara_cluster", "t-test", "Peak shapes",
    "Fast peak shapes", "PCA features", "PCA samples", "mzMatch"),
  normalize = T,
  useNormalized = T,
  logNormalized = F,
  MSData = NULL,
  ppm = 5,
  controlGroup = NULL,
  numClusters = 2,
  mzMatchParam = list("smid-db_pos.csv", ppm = 5, mzdiff = 0.001),
  workers = 1
)

Arguments

df	a data.frame with numeric (intensity) values, rt and mz values
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
MSData	a (named) list of xcmsRaw objects, e.g. generated by Mseek::loadRawM, OR an MSnbase OnDiskMSnExp object required for peak shape 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

Value

df with additional columns (or overridden columns) as generated by the selected analyses

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