Support for building BiblioSpec libraries from MeroX proxl.xml files. #2388
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If a crosslinker has any neutral losses defined, it is assumed that those neutral losses result in the crosslinker being cleaved.
…k/20221117_BlibMeroXSupport
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Sorry for the delay. The blib changes look fine except for tabs. I'm looking into the MGF TITLE thing. It looks like SpectrumList::findSpotId does look up spectrum titles. But it requires the full title, not just a substring from it. That can be augmented though to address the MGF scan number issue you emailed about.
| case PERCOLATOR_ANALYSIS: return blibMaker_.getScoreThreshold(GENERIC_QVALUE_INPUT); | ||
| case PLINK_ANALYIS: return blibMaker_.getScoreThreshold(GENERIC_QVALUE_INPUT); | ||
| case BYONIC_ANALYSIS: | ||
| return blibMaker_.getScoreThreshold(BYONIC); |
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I guess your C# tab settings didn't get carried over to the C++ editor. :)
| @@ -107,6 +107,8 @@ void ProxlXmlReader::startElement(const XML_Char* name, const XML_Char** attr) { | |||
| analysisType_ = BYONIC_ANALYSIS; | |||
| else if (program == "plink") | |||
| analysisType_ = PLINK_ANALYIS; | |||
| else if (program == "merox") | |||
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I guess your C# tab settings didn't get carried over to the C++ editor. :)
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Hi @nickshulman , Looks like you actually added support for this variant of proXL. Do you remember why you picked "qvalue" instead of "score"? |
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We usually do use a q value when it is present. We rarely use a native
score. What is "score"? Is it a probability value? If so what kind? e.g
expectation, posterior error probability, etc.
…On Mon, Nov 27, 2023 at 10:23 AM Matt Chambers ***@***.***> wrote:
Hi @nickshulman <https://github.com/nickshulman> ,
Looks like you actually added support for this variant of proXL. Do you
remember why you picked "qvalue" instead of "score"?
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MeroX Score. According to Juan it's calculated across multiple files. Looks like it might be a -log score of expectation or probability (higher is better). |
Added support for building spectral libraries from MeroX proxl.xml files (requested by Juan)
(still need to add a BiblioSpec unit test)