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Run QC on input data

QCData.Rd

Run QC on input data

Usage

QCData(
  inputData,
  filterBlanks = TRUE,
  filterExtraction = TRUE,
  blankFoldThreshold = 5,
  naTolerance = 0.05,
  blankPattern = "^PB|blank",
  controlPattern = "^PB|^TC|^QC"
)

Arguments

inputData

Input metabolite data

filterBlanks

Whether to run blank filtering. See FilterBlanks().

filterExtraction

Whether to filter for the best extraction method. See FilterExtraction().

blankFoldThreshold

The blank fold change threshold. The difference between every metabolite and its batch's blank must be at least this value or higher to remain in the dataset.

naTolerance

The absolute acceptable non-NA proportion difference for a given metabolite across separation methods like IP, HILICA and T3Acidic. Metabolites with proportion differences under this value will be picked based on their coefficient of variance. See FilterExtraction().

blankPattern

String pattern to denote blank samples

controlPattern

String pattern to denote control samples like QC

Details

For each metabolite's separation method, it selects the one with the lowest proportion NAs, or if similar proportions, the lowest coefficient of variance. See FilterExtraction(). Then removes

  • data points below a fold change threshold compared to blank samples. See BlankFilter().

  • metabolites with zero variance

  • Blank samples (after blank filtering)

  • Control samples