outlierFind: ================================================================...
In mooredf22/protsummarize2:

Description Usage Arguments

View source: R/OutlierFind.R

================================================================ OutlierFind to identify outliers in a matrix using both scoresMod and boxplotMod

outlierFind(
  protClass = tannousSpectral,
  outlierLevel = "peptide",
  refCol = 5,
  nCol = 9,
  outlierMeth = "boxplot",
  range = 3,
  proba = 0.99,
  eps = eps,
  cpus = 4,
  randomError = F
)

`protClass:`	a matrix of protein, peptide identifiers and normalized specific amounts
`outlierLevel:`	peptide for outlier spectra within peptides, or protein for outlier peptides within proteins'
`refCol:`	number of columns before Mass Spectrometry data columns
`nCol:`	how many columns in MS data
`outlierMeth:`	boxplot (recommended), scores, or none
`range:`	the range parameter used for identifying outliers
`eps:`	value to add before log2 transfromations (to avoid taking log of zero)
`cpus:`	number of cpus to use for parallel processing