Skyline/work/20230710 add refine with shape correlation #2663
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…antizationCutoff parameters
…lue below test cutoff
…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20230710_addRefineWithShapeCorrelation
nickshulman
reviewed
Jul 17, 2023
|
Let's make it "refine-shape-r-include-cutoff" and
"refine-shape-r-quant-cutoff". We don't need to spell everything out
completely in the argument name. That is what the description is for. There
is some value to keeping these argument names shorter. For one, they fit
the documentation table layout better.
…On Mon, Jul 17, 2023 at 10:19 AM nickshulman ***@***.***> wrote:
***@***.**** commented on this pull request.
------------------------------
In pwiz_tools/Skyline/CommandArgs.cs
<#2663 (comment)>:
> @@ -902,6 +902,10 @@ private bool ParseReintegrateExcludeFeature(NameValuePair pair)
(c, p) => c.Refinement.QValueCutoff = p.ValueDouble);
public static readonly Argument ARG_REFINE_MINIMUM_DETECTIONS = new RefineArgument(@"refine-minimum-detections", INT_VALUE,
(c, p) => c.Refinement.MinimumDetections = p.ValueInt);
+ public static readonly Argument ARG_REFINE_SC_INCLUDED_CUTOFF = new RefineArgument(@"refine-shape-correlation-included-cutoff", NUM_VALUE,
+ (c, p) => c.Refinement.SCIncludedCutoff = p.ValueDouble);
+ public static readonly Argument ARG_REFINE_SC_QUANTIZATION_CUTOFF = new RefineArgument(@"refine-shape-correlation-quantization-cutoff", NUM_VALUE,
I think the word here should be "quantitative".
Transitions with a shape correlation below this value will be marked as
non-quantitative.
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…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20230710_addRefineWithShapeCorrelation
…o ComparisonType.min
nickshulman
reviewed
Jul 27, 2023
| { | ||
| if (type == ComparisonType.min) | ||
| { | ||
| comparisonValue = chromInfos.Min(c => c.PeakShapeValues?.ShapeCorrelation); |
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I think this will end up doing the wrong thing if any of the shape correlation values are null.
For the purposes of "Min", "null" is considered lower than any other number.
However, in terms of "<" or ">", comparison of null to a number is always false.
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Thanks for pointing this out. I changed the method to now check if shape correlation values are above the cutoff. If the method returns false the transition will be removed. Now when the comparison value is null the method will return false and the transition will be removed.
…or null SC values
…ttps://github.com/ProteoWizard/pwiz into Skyline/work/20230710_addRefineWithShapeCorrelation
…k/20230710_addRefineWithShapeCorrelation
…k/20230710_addRefineWithShapeCorrelation
…k/20230710_addRefineWithShapeCorrelation
…sources.resx Change "ARG_REFINE_SC_INCLUDED_COMPARISON_TYPE" to use "ComparisonType" enum.
…k/20230710_addRefineWithShapeCorrelation
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Added 2 parameters to the consistency tab of the RefineDlg. IncludedCutoff removes all transitions with a shape correlation below the cutoff value. QuantizationCutoff marks all transitions with a shape correlation below the value as non-quantitative.