make DEA
Examples
# example code
pep <- prolfqua::sim_lfq_data_protein_config()
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done
pep <- prolfqua::LFQData$new(pep$data, pep$config)
pA <- data.frame(protein_Id = unique(pep$data$protein_Id))
pA <- pA |> dplyr::mutate(fasta.annot = paste0(pA$protein_Id, "_description"))
pA <- prolfquapp::ProteinAnnotation$new(pep, row_annot = pA, description = "fasta.annot")
#> Warning: no exp_nr_children column specified, computing using nr_obs_experiment function
GRP2 <- prolfquapp::make_DEA_config_R6()
pep$factors()
#> # A tibble: 12 × 3
#> sample sampleName group_
#> <chr> <chr> <chr>
#> 1 A_V1 A_V1 A
#> 2 A_V2 A_V2 A
#> 3 A_V3 A_V3 A
#> 4 A_V4 A_V4 A
#> 5 B_V1 B_V1 B
#> 6 B_V2 B_V2 B
#> 7 B_V3 B_V3 B
#> 8 B_V4 B_V4 B
#> 9 Ctrl_V1 Ctrl_V1 Ctrl
#> 10 Ctrl_V2 Ctrl_V2 Ctrl
#> 11 Ctrl_V3 Ctrl_V3 Ctrl
#> 12 Ctrl_V4 Ctrl_V4 Ctrl
GRP2$pop <- list(Contrasts = c("AVsC" = "group_A - group_Ctrl", BVsC = "group_B - group_Ctrl"))
grp <- make_DEA_report2(pep, pA, GRP2)
#> INFO [2026-02-25 16:35:58] Transforming using log2
#> Column added : log2_abundance
#> INFO [2026-02-25 16:35:58] Transforming data : none.
#> abundance already in data : sample sampleName group_ isotopeLabel protein_Id abundance qValue nr_peptides .
#> FORMULA :normalized_abundance ~ group_
#> Joining with `by = join_by(protein_Id)`
#> INFO [2026-02-25 16:35:58] fitted model with formula : normalized_abundance ~ group_
#> determine linear functions:
#> Warning: Warn 'linfct_matrix_contrasts':In argument: `AVsC = group_A - group_Ctrl`.
#> Warning: Warn 'linfct_matrix_contrasts':In argument: `BVsC = group_B - group_Ctrl`.
#> Warning: Warn 'linfct_matrix_contrasts':In argument: `avg_AVsC = (group_A + group_Ctrl)/2`.
#> Warning: Warn 'linfct_matrix_contrasts':In argument: `avg_BVsC = (group_B + group_Ctrl)/2`.
#> get_contrasts -> contrasts_linfct
#> contrasts_linfct
#> Joining with `by = join_by(protein_Id, contrast)`
#> completing cases
#> AVsC=group_A - group_Ctrl
#> BVsC=group_B - group_Ctrl
#> AVsC=group_A - group_Ctrl
#> BVsC=group_B - group_Ctrl
#> AVsC=group_A - group_Ctrl
#> BVsC=group_B - group_Ctrl
#> Joining with `by = join_by(protein_Id, contrast)`
#> Joining with `by = join_by(protein_Id, contrast)`
#> Joining with `by = join_by(protein_Id)`