Cenerate instances of AnalysisTableAnnotation

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).

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, AnalysisParameters, AnalysisTableAnnotation, 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()

Examples

skylineconfig <- create_config_Skyline()
skylineconfig$table$factors[["Time"]] = "Sampling.Time.Point"
skylineconfig$table$factor_keys()
#> [1] "Time"
skylineconfig$table$hierarchy_keys()
#> [1] "protein_Id"   "peptide_Id"   "precursor_Id" "fragment_Id" 
spectronautconfig <- create_config_Spectronaut_Peptide()
config <- create_config_Spectronaut_Peptide()
config$table$factors[["coding"]] = "coding"
config$table$factors[["sex"]] = "sex"
config$table$factors[["age"]] = "age"
config$table$factors[["Sample_id"]] = "Sample.Name"

tmp <- create_config_MQ_peptide()

create_config_MSFragger_MSstats()
#> <AnalysisConfiguration>
#>   Public:
#>     clone: function (deep = FALSE) 
#>     initialize: function (analysisTableAnnotation, analysisParameter = AnalysisParameters$new()) 
#>     parameter: AnalysisParameters, R6
#>     sep: ~
#>     table: AnalysisTableAnnotation, R6