Usage
MaxQtoMSstatsFormat(evidence, annotation,proteinGroups, proteinID="Proteins", useUniquePeptide=TRUE, summaryforMultipleRows=max, fewMeasurements="remove", removeMpeptides=TRUE)
Arguments
evidence
name of 'evidence.txt' data, which includes feature-level data.
annotation
name of 'annotation.txt' data which includes Raw.file, Condition, BioReplicate, Run, IsotopeLabelType information.
proteinGroups
name of 'proteinGroups.txt' data. It needs to matching protein group ID. If proteinGroups=NULL, use 'Proteins' column in 'evidence.txt'.
proteinID
'Proteins'(default) or 'proteinGroups' in 'proteinGroup.txt' for Protein ID.
useUniquePeptide
TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
summaryforMultipleRows
max(default) or sum - when there are multiple measurements for certain feature and certain fun, use highest or sum of all.
fewMeasurements
'remove'(default) will remove the features that have 1 or 2 measurements across runs. It can affect 'dataProcess' function with unequal variance between features option.
removeMpeptides
TRUE(default) will remove the peptides including 'M' sequence.