DRY function: process and export annotated contrasts

DRY function: process and export annotated contrasts

Usage

annotation_add_contrasts(
  df,
  primary_col,
  secondary_col,
  prefix = "G_",
  dataset_id = "dataset",
  decreasing = FALSE,
  interactions = TRUE
)

Arguments

df

data.frame with annotation data

primary_col

character, name of the primary factor column

secondary_col

character, name of the secondary factor column

prefix

character, prefix for output naming (default "G_")

dataset_id

character, dataset identifier for output naming

decreasing

logical, if TRUE sort factor levels in decreasing order

interactions

logical, if TRUE include interaction contrasts

Value

Contrast definitions or contrast results.

See also

Other contrasts: generate_contrasts(), generate_contrasts_for_factor(), interaction_contrasts(), level_specific_contrasts(), main_effect_contrasts()

Examples

data("x5463yzwer453bbb", package = "prolfqua")
annotation_add_contrasts(x5463yzwer453bbb, "factor_A", "factor_B", "primary")
#> $annot
#> # A tibble: 36 × 5
#>    `Relative Path`                             Name  Group ContrastName Contrast
#>  * <chr>                                       <chr> <chr> <chr>        <chr>   
#>  1 20250429_019_C38312-12_S935004_MI_150_6_S1… MI_1… MI_T… MINOCA_vs_MI ( (G_MI…
#>  2 20250429_003_C38312-21_S935013_MINOCA_0_3_… MINO… MINO… MINOCA_vs_M… G_MINOC…
#>  3 20250429_015_C38312-35_S935027_MINOCA_300_… MINO… MINO… MINOCA_vs_M… G_MINOC…
#>  4 20250429_016_C38312-11_S935003_MI_150_5_S1… MI_1… MI_T… MINOCA_vs_M… G_MINOC…
#>  5 20250429_014_C38312-7_S934999_MI_150_1_S1-… MI_1… MI_T… interaction… (G_MINO…
#>  6 20250429_035_C38312-3_S934995_MI_0_3_S1-C1… MI_0… MI_T0 interaction… (G_MINO…
#>  7 20250429_022_C38312-25_S935017_MINOCA_150_… MINO… MINO… interaction… (G_MINO…
#>  8 20250429_043_C38312-14_S935006_MI_300_2_S1… MI_3… MI_T… NA           NA      
#>  9 20250429_004_C38312-29_S935021_MINOCA_150_… MINO… MINO… NA           NA      
#> 10 20250429_034_C38312-15_S935007_MI_300_3_S1… MI_3… MI_T… NA           NA      
#> # ℹ 26 more rows
#> 
#> $name
#> [1] "DEA_primary_dataset.csv"
#> 
annotation_add_contrasts(x5463yzwer453bbb, "factor_B", "factor_A", "secondary")
#> $annot
#> # A tibble: 36 × 5
#>    `Relative Path`                             Name  Group ContrastName Contrast
#>  * <chr>                                       <chr> <chr> <chr>        <chr>   
#>  1 20250429_019_C38312-12_S935004_MI_150_6_S1… MI_1… T150… T150_vs_T0   ( (G_T1…
#>  2 20250429_003_C38312-21_S935013_MINOCA_0_3_… MINO… T0_M… T300_vs_T0   ( (G_T3…
#>  3 20250429_015_C38312-35_S935027_MINOCA_300_… MINO… T300… T300_vs_T150 ( (G_T3…
#>  4 20250429_016_C38312-11_S935003_MI_150_5_S1… MI_1… T150… T150_vs_T0_… G_T150_…
#>  5 20250429_014_C38312-7_S934999_MI_150_1_S1-… MI_1… T150… T150_vs_T0_… G_T150_…
#>  6 20250429_035_C38312-3_S934995_MI_0_3_S1-C1… MI_0… T0_MI T300_vs_T0_… G_T300_…
#>  7 20250429_022_C38312-25_S935017_MINOCA_150_… MINO… T150… T300_vs_T0_… G_T300_…
#>  8 20250429_043_C38312-14_S935006_MI_300_2_S1… MI_3… T300… T300_vs_T15… G_T300_…
#>  9 20250429_004_C38312-29_S935021_MINOCA_150_… MINO… T150… T300_vs_T15… G_T300_…
#> 10 20250429_034_C38312-15_S935007_MI_300_3_S1… MI_3… T300… interaction… (G_T150…
#> # ℹ 26 more rows
#> 
#> $name
#> [1] "DEA_secondary_dataset.csv"
#>