Widgets to set parameters for quantification and statistics

[veitveit]

That would be FDRs for PSMs, protein (#15 ) and statistical analysis by LIMMA. Other potentially interesting parameters:

• Summarization method
• Min. peptides per protein
• PTMs used for quantification

The FDR from LIMMA can be set directly in an interactive shiny app that adapts the volcano plots to the parameter.

[jgriss]

About the third item: Do you mean that users should be able to select which (variable) PTMs they want to include for quant or whether they want to include modified peptides?

[veitveit]

I thought about which PTMs to include for quant (e.g. oxidations yes or no).
Quantifying PTMs would be really great to include at some point but not yet

[jgriss]

OK. I've now added a checkbox to indicate whether modified PSMs should be included. Adding one checkbox / PTM is a little more work and is only possible, once the user selected which PTMs to include in the search.

If you agree, I'd stick with this simple version for the first milestone and then, if we want, add the fancier version later on. Does that sound OK?

[veitveit]

Sure :-)

2018-05-16 19:07 GMT+02:00 Johannes Griss notifications@github.com:

OK. I've now added a checkbox to indicate whether modified PSMs should be included. Adding one checkbox / PTM is a little more work and is only possible, once the user selected which PTMs to include in the search.

If you agree, I'd stick with this simple version for the first milestone and then, if we want, add the fancier version later on. Does that sound OK?

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