protProfileSummarize: ================================================================...
In mooredf22/protsummarize2:

================================================================ protProfileSummarize calculates mean and SE for each channel in each prot using random effect model or arithmetic mean random effect model can avoid dominance of a sequence with too many spectra

protProfileSummarize(
  protsCombineCnew,
  refCol,
  nCol,
  refColsKeep = c(1, 2),
  eps,
  GroupBy = "protId",
  outlierExclude = "spectraAndPeptide",
  logDataOut = F,
  cpus = 4
)

`protsCombineCnew:`	a matrix of protein information and normalized specific amounts and outlier information
`refCol:`	number of columns before Mass Spectrometry data columns
`nCol:`	how many columns in MS data
`eps:`	epsilon to avoid log(0)
`GroupBy:`	"protId" if average by protein; "peptideId" if average by peptide
`outlierExclude:`	"none", "spectra" (default), or "spectraAndpeptide according to exclusion level
`cpus:`	number of cpus to use for parallel processing