MQtoMSstatsFormat: MaxQtoMSstatsFormat
In protViz/SRMService: Report Quantitative Mass Spectrometry Data

MaxQtoMSstatsFormat

MQtoMSstatsFormat(
  evidence,
  annotation,
  proteinGroups,
  useUniquePeptide = TRUE,
  summaryforMultipleRows = max,
  fewMeasurements = "remove",
  removeMpeptides = TRUE
)

`evidence`	MQ evidence.txt read using read.csv(sep=\"\t\")
`annotation`	data.frame with columns Raw.file, Condition, BioReplicate, Run, IsotopeLabelType
`proteinGroups`	provide MQ proteinGroups.txt
`useUniquePeptide`	: (likely same as proteotypic) remove peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
`summaryforMultipleRows`	: max or sum - when there are multiple measurements for certain feature and certain fun, use highest or sum of all.
`fewMeasurements`	: if 1 or 2 measurements across runs per feature, 'remove' will remove those featuares. It can affected for unequal variance analysis.
`removeMpeptides`	remove remove the peptides including M sequence