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Generate instances of AnalysisConfiguration

Source: R/tidyMS_R6_ConcreteConfigurations.R
concrete_AnalysisConfiguration.Rd

configurations examples of or various signal processing software outputs

file must be read with tidyMQ_Peptides, you will still need to add the factors (explanatory variables).

Usage

create_config_Skyline(
  isotopeLabel = "Isotope.Label",
  ident_qValue = "annotation_QValue"
)

create_config_Spectronaut_Peptide(
  isotopeLabel = "Isotope.Label",
  ident_qValue = "EG.Qvalue"
)

create_config_MQ_peptide(
  ident_qValue = "pep",
  intensity = "peptide.intensity",
  isotopeLabel = "isotope"
)

create_config_MSFragger_MSstats()

Arguments

isotopeLabel

isotope

ident_qValue

pep

intensity

peptide.intensity

See also

Other configuration: AnalysisConfiguration, INTERNAL_FUNCTIONS_BY_FAMILY, R6_extract_values(), complete_cases(), make_interaction_column(), make_reduced_hierarchy_config(), sample_subset(), separate_factors(), separate_hierarchy(), setup_analysis(), spread_response_by_IsotopeLabel(), table_factors(), table_factors_size()

Examples

skylineconfig <- create_config_Skyline()
skylineconfig$factors[["Time"]] = "Sampling.Time.Point"
skylineconfig$factor_keys()
#> [1] "Time"
skylineconfig$hierarchy_keys()
#> [1] "protein_Id"   "peptide_Id"   "precursor_Id" "fragment_Id" 



spectronautconfig <- create_config_Spectronaut_Peptide()
config <- create_config_Spectronaut_Peptide()
config$factors[["coding"]] = "coding"
config$factors[["sex"]] = "sex"
config$factors[["age"]] = "age"
config$factors[["Sample_id"]] = "Sample.Name"

tmp <- create_config_MQ_peptide()

create_config_MSFragger_MSstats()
#> <AnalysisConfiguration>
#>   Public:
#>     annotation_vars: function () 
#>     bin_resp: 
#>     clone: function (deep = FALSE) 
#>     factorDepth: 1
#>     factor_keys: function () 
#>     factor_keys_depth: function () 
#>     factors: list
#>     fileName: Run
#>     get_response: function () 
#>     hierarchy: list
#>     hierarchyDepth: 1
#>     hierarchyKeys: function (rev = FALSE) 
#>     hierarchy_keys: function (rev = FALSE) 
#>     hierarchy_keys_depth: function (names = TRUE) 
#>     hkeysDepth: function (names = TRUE) 
#>     id_required: function () 
#>     id_vars: function () 
#>     ident_Score: 
#>     ident_qValue: pep
#>     initialize: function (analysisTableAnnotation = NULL, analysisParameter = NULL) 
#>     is_response_transformed: FALSE
#>     isotopeLabel: IsotopeLabelType
#>     min_peptides_protein: 2
#>     normValue: NULL
#>     nr_children: nr_children
#>     opt_mz: 
#>     opt_rt: 
#>     parameter: active binding
#>     pop_response: function () 
#>     sampleName: sampleName
#>     sep: ~
#>     set_response: function (colName) 
#>     table: active binding
#>     value_vars: function () 
#>     workIntensity: Intensity