Use different rt_tol for uncorrected rt

src/SphingolipidsID.jl

@@ -412,19 +412,20 @@ propertynames(quant::Quantification) = (:batch, :config, propertynames(getfield(
 """
  RTCorrection
 
-Type holding rt data and regression line for correcting rt from old batch (data for identification) to new batch (data for quantification).
+Type holding rt data and regression line for correcting rt from new batch (data for quantification) to old batch (data for identification).
 
-* `formula`: formula of regression line.
 * `data`: raw data from new batch.
 * `table`: old transition table generated from `project.analyte` and function `analytetable_mrm`.
-* `fn`: `Dictionary` containg regression coefficents for each class.
+* `model`: `Dictionary` containg regression coefficents for each class.
+* `config`: `Dictionary` containgin configuration.
 
 This is a callable object taking a class and rt or vector of class and a vector of rt as input, and returning new rt or a vector of new rt. If the class is not in `fn`, it will return the original rt. 
 """
 struct RTCorrection
  data::AbstractRawData
  table::Table
  model::Dictionary
+ config::Dictionary
 end
 (fn::RTCorrection)(cls::ClassSP, dt) = model_predict(get(fn.model, cls, nothing), dt)
 (fn::RTCorrection)(cls::Vector{<: ClassSP}, dt) = mapreduce(vcat, cls, dt) do c, d

src/quantification.jl

@@ -121,13 +121,14 @@ end
 function set_qcdata_mrm!(project::Project, featuretable::Table; 
  rt_correction = nothing,
  rt_tol = last(project.data).config[:rt_tol], 
+ raw_rt_tol = isnothing(rt_correction) ? 0.3 : rt_correction.config[:rt_tol],
  mz_tol = last(project.data).config[:mz_tol], 
  signal = project.appendix[:signal],
  est_fn = mean, 
  err_fn = rsd, 
  err_tol = 0.5,
  other_fn = Dictionary{Symbol, Any}())
- push!(project.data, qcdata_mrm!(featuretable, project; rt_correction, rt_tol, mz_tol, signal, est_fn, err_fn, err_tol, other_fn))
+ push!(project.data, qcdata_mrm!(featuretable, project; rt_correction, rt_tol, raw_rt_tol, mz_tol, signal, est_fn, err_fn, err_tol, other_fn))
  set!(project.quantification.config, :qcdata, last(project.data))
  last(project.data)
 end
@@ -138,6 +139,7 @@ qcdata_mrm!(project::Project, featuretable::Table; kwargs...) = qcdata_mrm!(feat
 function qcdata_mrm!(featuretable::Table, project = nothing;
  rt_correction = nothing, 
  rt_tol = isnothing(project) ? 0.1 : last(project.data).config[:rt_tol], 
+ raw_rt_tol = isnothing(rt_correction) ? 0.3 : rt_correction.config[:rt_tol],
  mz_tol = isnothing(project) ? 0.35 : last(project.data).config[:mz_tol], 
  signal = isnothing(project) ? :area : project.appendix[:signal],
  est_fn = mean, 
@@ -152,7 +154,7 @@ function qcdata_mrm!(featuretable::Table, project = nothing;
  end
  other_fn = default_other_fn
  n = length(unique(featuretable.datafile))
- mrm = MRM!(Table(featuretable; match_id = zeros(Int, length(featuretable)), match_score = -getproperty(featuretable, signal)); combine = false, rt_tol, mz_tol, n = 1, signal = nothing, est_fn, err_fn, err_tol, other_fn)
+ mrm = MRM!(Table(featuretable; match_id = zeros(Int, length(featuretable)), match_score = -getproperty(featuretable, signal)); combine = false, rt_tol = raw_rt_tol, mz_tol, n = 1, signal = nothing, est_fn, err_fn, err_tol, other_fn)
  transition_matching!(mrm, project; rt_correction, rt_tol, mz_tol)
  at = analysistable(mrm.table; method = mrm.config[:method], data = signal)
  if !isnothing(project)
@@ -174,13 +176,14 @@ function set_serialdilution_mrm!(project::Project, featuretable::Table, concentr
  r2_threshold = 0.8,
  nlevel = 5,
  rt_tol = last(project.data).config[:rt_tol], 
+ raw_rt_tol = isnothing(rt_correction) ? 0.3 : rt_correction.config[:rt_tol],
  mz_tol = last(project.data).config[:mz_tol], 
  signal = project.appendix[:signal],
  est_fn = mean, 
  err_fn = rsd, 
  err_tol = 0.5,
  other_fn = Dictionary{Symbol, Any}())
- push!(project.data, serialdilution_mrm!(featuretable, concentration, project; pointlevel, rt_correction, r2_threshold, nlevel, rt_tol, mz_tol, signal, est_fn, err_fn, err_tol, other_fn))
+ push!(project.data, serialdilution_mrm!(featuretable, concentration, project; pointlevel, rt_correction, r2_threshold, nlevel, rt_tol, raw_rt_tol, mz_tol, signal, est_fn, err_fn, err_tol, other_fn))
  set!(project.quantification.config, :serialdilution, last(project.data))
  last(project.data)
 end
@@ -195,6 +198,7 @@ function serialdilution_mrm!(featuretable::Table, concentration::Vector, project
  r2_threshold = 0.8,
  nlevel = 5,
  rt_tol = isnothing(project) ? 0.1 : last(project.data).config[:rt_tol], 
+ raw_rt_tol = isnothing(rt_correction) ? 0.3 : rt_correction.config[:rt_tol],
  mz_tol = isnothing(project) ? 0.35 : last(project.data).config[:mz_tol], 
  signal = isnothing(project) ? :area : project.appendix[:signal],
  est_fn = mean, 
@@ -208,7 +212,7 @@ function serialdilution_mrm!(featuretable::Table, concentration::Vector, project
  end
  end
  other_fn = default_other_fn
- mrm = MRM!(Table(featuretable; match_id = zeros(Int, length(featuretable)), match_score = -getproperty(featuretable, signal)); combine = false, rt_tol, mz_tol, n = 1, signal = nothing, est_fn, err_fn, err_tol, other_fn)
+ mrm = MRM!(Table(featuretable; match_id = zeros(Int, length(featuretable)), match_score = -getproperty(featuretable, signal)); combine = false, rt_tol = raw_rt_tol, mz_tol, n = 1, signal = nothing, est_fn, err_fn, err_tol, other_fn)
  transition_matching!(mrm, project; rt_correction, rt_tol, mz_tol)
  config = dictionary(pairs((; concentration, rt_correction, r2_threshold, nlevel, rt_tol, mz_tol, signal, est_fn, err_fn, err_tol, other_fn)))
  at = analysistable(mrm.table; method = mrm.config[:method], data = signal)
@@ -286,13 +290,14 @@ function set_quantdata_mrm!(project::Project, featuretable::Table;
  rt_correction = nothing,
  name = r"S\d*.*",
  rt_tol = last(project.data).config[:rt_tol], 
+ raw_rt_tol = isnothing(rt_correction) ? 0.3 : rt_correction.config[:rt_tol],
  mz_tol = last(project.data).config[:mz_tol], 
  signal = project.appendix[:signal],
  est_fn = mean, 
  err_fn = rsd, 
  err_tol = 0.5,
  other_fn = Dictionary{Symbol, Any}())
- push!(project.data, quantdata_mrm!(featuretable, project; rt_correction, name, rt_tol, mz_tol, signal, est_fn, err_fn, err_tol, other_fn))
+ push!(project.data, quantdata_mrm!(featuretable, project; rt_correction, name, rt_tol, raw_rt_tol, mz_tol, signal, est_fn, err_fn, err_tol, other_fn))
  set!(project.quantification.config, :quantdata, last(project.data))
  last(project.data)
 end
@@ -303,6 +308,7 @@ quantdata_mrm!(project::Project, featuretable::Table; kwargs...) = quantdata_mrm
 function quantdata_mrm!(featuretable::Table, project = nothing;
  rt_correction = nothing, 
  rt_tol = isnothing(project) ? 0.1 : last(project.data).config[:rt_tol], 
+ raw_rt_tol = isnothing(rt_correction) ? 0.3 : rt_correction.config[:rt_tol],
  mz_tol = isnothing(project) ? 0.35 : last(project.data).config[:mz_tol], 
  signal = isnothing(project) ? :area : project.appendix[:signal],
  est_fn = mean, 
@@ -317,7 +323,7 @@ function quantdata_mrm!(featuretable::Table, project = nothing;
  end
  other_fn = default_other_fn
  n = length(unique(featuretable.datafile))
- mrm = MRM!(Table(featuretable; match_id = zeros(Int, length(featuretable)), match_score = -getproperty(featuretable, signal)); combine = false, rt_tol, mz_tol, n = 1, signal = false, est_fn, err_fn, err_tol, other_fn)
+ mrm = MRM!(Table(featuretable; match_id = zeros(Int, length(featuretable)), match_score = -getproperty(featuretable, signal)); combine = false, rt_tol = raw_rt_tol, mz_tol, n = 1, signal = false, est_fn, err_fn, err_tol, other_fn)
  transition_matching!(mrm, project; rt_correction, rt_tol, mz_tol)
  at = analysistable(mrm.table; method = mrm.config[:method], data = signal)
  if !isnothing(project)

src/rt.jl

@@ -413,7 +413,7 @@ rt_correction(modelcall::RetentionModelCall, data::AbstractRawData, analytetable
 function rt_correction(modelcall::RetentionModelCall, analytetable::Table, data::AbstractRawData; mz_tol = 0.35, rt_tol = 0.3)
  RTCorrection(data, analytetable, map(groupview(x -> class(x.analyte), analytetable)) do tbl
  rt_correction_modeling(modelcall, tbl, data; rt_tol, mz_tol)
- end)
+ end, Dictionary([:rt_tol, :mz_tol], [rt_tol, mz_tol]))
 end
 
 function rt_correction_modeling(modelcall, tbl, data; rt_tol, mz_tol)
@@ -439,7 +439,7 @@ function rt_correction_modeling(modelcall, tbl, data; rt_tol, mz_tol)
 end
 
 function update_rt_correction!(rc::RTCorrection, modelcall::RetentionModelCall, cls::ClassSP)
- set!(rc.model, cls, @views rt_correction_modeling(modelcall, rc.table[class.(rc.table.analyte) .== cls], rc.data))
+ set!(rc.model, cls, @views rt_correction_modeling(modelcall, rc.table[class.(rc.table.analyte) .== cls], rc.data; rt_tol = rc.config[:rt_tol], mz_tol = rc.config[:mz_tol]))
  rc
 end