When the supplied PEPs contain missing values, computeFDR breaks and throws an error. However, MaxQuant does not compute PEPs for PSMs that were identified using the match between run algorithm. So, computeFDR must be adapted in order to:
Not break due to an error (eventually print a message or warning)
Account for missing PEP (e.g. setting na.rm = TRUE)
When the supplied PEPs contain missing values,
computeFDRbreaks and throws an error. However, MaxQuant does not compute PEPs for PSMs that were identified using the match between run algorithm. So,computeFDRmust be adapted in order to:na.rm = TRUE)