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Compute fold changes given Contrasts

Source: R/tidyMS_missingness_summary.R
get_contrast.Rd

Compute fold changes given Contrasts

Usage

get_contrast(data, hierarchy_keys, contrasts)

Arguments

data

hierarchy_keys of Analysis Configuration

contrasts

list of contrasts to compute

See also

Other imputation: missigness_histogram(), missingness_per_condition(), missingness_per_condition_cumsum(), upset_interaction_missing_stats(), upset_missing_stats()

Examples



istar <- sim_lfq_data_peptide_config()
#> creating sampleName from file_name column
#> completing cases
#> completing cases done
#> setup done
lfq <- LFQData$new(istar$data, istar$config)
lfq$complete_cases()
#> completing cases

Contrasts <- c("dilution.b-a" = "group_A - group_B", "dilution.c-e" = "group_A - group_Ctrl")

var <- summarize_stats(lfq)
var <- prolfqua::make_interaction_column(var, columns = lfq$relevant_factor_keys())

imp <- var |> tidyr::pivot_wider(id_cols = lfq$hierarchy_keys(),
                        names_from = interaction,
                        values_from = !!rlang::sym("meanAbundance"))

imputed <- get_contrast(imp, lfq$hierarchy_keys(), Contrasts)
#> dilution.b-a=group_A - group_B
#> dilution.c-e=group_A - group_Ctrl