vitek-lab / msstatsconvert Goto Github PK
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Home Page: https://Vitek-Lab.github.io/MSstatsConvert
Converter functions for the MSstats package
Home Page: https://Vitek-Lab.github.io/MSstatsConvert
If annotation is taken from the input, remove Condition and BioReplicate columns or make a flag for this
Remove the parameter rmPSM_withMissing_withinRun = FALSE and all related codes from TMT converters
it will be helpful
Decide, what should be the class of the output (some operations on df may not work with DT) [backward-compatibility]
in summarize multiple measurements
and aggregate isotopic peaks
dcast vs current
In Skyline converter, missing intensities were only filtered in DDA case:
input <- input[!is.na(input$Intensity), ]
(line 183 in the original file)
Check if the same happened in other converters, be consistent
Check gSheet for LF
fractions + fill incomplete rows
Sometimes the user doesn't have permission to create a file
Early in the MSstatsPreprocess function
Consistent names
for example as in DDA-Meierhofer2016 benchmark dataset for MaxQuant
there are identifcal rows in the input that pass all the tests in .aggregatePSMstoPeptideIons -> output has duplicated rows
before release
yes or no?
PD:
PDTMT:
(above? +)
Spectronaut:
this happens in some converters, for example PD - there should be an option to remove rows with multiple protein IDs
add it to Condition column with a double underscore separator
TODO: this should be happening on load, because we don't know yet if the user want to append?
OR if we don't save at this moment, the file won't be created, yet - file name can go to options, too?
particularly in TMT converters
remember about size restrictions for the package
LF converter : fewMeasurement option -> removeFewMeasurements or removefeaMeasurement and TRUE/FALSE.
The separator can be different for different tools.
Shared peptides here?
Check this when validating the results and fix
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