transform long to wide
tidy_to_wide_config(
data,
config,
as.matrix = FALSE,
fileName = FALSE,
sep = "~lfq~",
value = config$table$get_response()
)list with data, rowdata, and annotation (colData)
dd <- prolfqua::sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> Warning: no nr_children column specified in the data, adding column nr_children and setting to 1.
#> completing cases
config <- dd$config
data <- dd$data
res <- tidy_to_wide_config(data, config)
testthat::expect_equal(nrow(res$rowdata), nrow(res$data))
testthat::expect_equal(ncol(res$data) - ncol(res$rowdata) , nrow(res$annotation))
res <- tidy_to_wide_config(data, config, as.matrix = TRUE)
stopifnot(all(dim(res$data) == c(28, 12)))
stopifnot(all(dim(res$annotation) == c(12, 4)))
stopifnot(all(dim(res$rowdata) == c(28, 3)))
res <- scale(res$data)
tidy_to_wide_config(data, config, value = config$table$nr_children)
#> $data
#> # A tibble: 28 × 15
#> protein_Id peptide_Id isotopeLabel A_V1 A_V2 A_V3 A_V4 B_V1 B_V2 B_V3
#> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0EfVhX~0087 ITLb4x1q light 1 NA 1 1 1 1 1
#> 2 0EfVhX~0087 ahQLlQY7 light 1 1 1 1 1 1 1
#> 3 0EfVhX~0087 dJkdz7so light NA 1 1 NA 1 1 1
#> 4 7cbcrd~5725 D5dQ4nKk light 1 1 1 1 NA 1 1
#> 5 9VUkAq~4703 eIC06D7g light 1 1 1 1 1 NA 1
#> 6 BEJI92~5282 HBkZvdhT light 1 1 NA NA 1 1 1
#> 7 BEJI92~5282 qQ1GK8Un light 1 1 1 1 1 1 1
#> 8 CGzoYe~2147 mjHSHhoe light 1 1 1 1 NA 1 1
#> 9 DoWup2~5896 KVUnZ6oZ light 1 1 1 1 1 1 1
#> 10 Fl4JiV~8625 GsUIOl6Q light 1 1 1 NA 1 1 1
#> # ℹ 18 more rows
#> # ℹ 5 more variables: B_V4 <dbl>, Ctrl_V1 <dbl>, Ctrl_V2 <dbl>, Ctrl_V3 <dbl>,
#> # Ctrl_V4 <dbl>
#>
#> $annotation
#> # A tibble: 12 × 4
#> sampleName sample group_ isotopeLabel
#> <chr> <chr> <chr> <chr>
#> 1 A_V1 A_V1 A light
#> 2 A_V2 A_V2 A light
#> 3 A_V3 A_V3 A light
#> 4 A_V4 A_V4 A light
#> 5 B_V1 B_V1 B light
#> 6 B_V2 B_V2 B light
#> 7 B_V3 B_V3 B light
#> 8 B_V4 B_V4 B light
#> 9 Ctrl_V1 Ctrl_V1 Ctrl light
#> 10 Ctrl_V2 Ctrl_V2 Ctrl light
#> 11 Ctrl_V3 Ctrl_V3 Ctrl light
#> 12 Ctrl_V4 Ctrl_V4 Ctrl light
#>
#> $rowdata
#> # A tibble: 28 × 3
#> protein_Id peptide_Id isotopeLabel
#> <chr> <chr> <chr>
#> 1 0EfVhX~0087 ITLb4x1q light
#> 2 0EfVhX~0087 ahQLlQY7 light
#> 3 0EfVhX~0087 dJkdz7so light
#> 4 7cbcrd~5725 D5dQ4nKk light
#> 5 9VUkAq~4703 eIC06D7g light
#> 6 BEJI92~5282 HBkZvdhT light
#> 7 BEJI92~5282 qQ1GK8Un light
#> 8 CGzoYe~2147 mjHSHhoe light
#> 9 DoWup2~5896 KVUnZ6oZ light
#> 10 Fl4JiV~8625 GsUIOl6Q light
#> # ℹ 18 more rows
#>
xt <- prolfqua::LFQData$new(dd$data, dd$config)
xt$data$nr_children
#> [1] 1 1 NA 1 1 1 1 1 1 1 1 NA 1 1 NA 1 1 1 1 1 1 1 1 1 1
#> [26] NA 1 NA NA 1 1 1 1 1 1 1 1 1 1 NA 1 1 1 1 1 1 1 1 1 1
#> [51] 1 1 1 1 1 1 1 1 1 1 1 NA 1 1 1 1 1 1 1 NA 1 1 1 1 1
#> [76] 1 1 1 1 1 1 1 1 NA 1 1 NA 1 1 NA 1 1 1 NA 1 NA 1 1 1 1
#> [101] 1 1 1 1 1 1 1 1 1 1 1 NA 1 1 1 NA 1 1 1 NA 1 1 1 1 1
#> [126] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 NA 1 1 1 1 1
#> [151] 1 1 1 1 1 1 1 1 1 1 1 1 NA 1 1 1 1 1 1 1 1 1 1 1 1
#> [176] 1 1 1 1 NA 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 NA 1 1
#> [201] 1 1 1 1 1 1 NA 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> [226] 1 NA 1 1 NA 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 NA 1 1 NA
#> [251] 1 1 1 NA 1 1 1 1 NA 1 1 NA 1 1 1 1 1 1 1 1 1 1 1 1 1
#> [276] 1 1 1 1 1 NA 1 1 NA 1 NA 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> [301] 1 1 1 1 1 NA 1 1 1 1 1 1 1 1 1 1 1 1 NA 1 1 1 NA 1 1
#> [326] 1 1 1 1 1 NA 1 1 1 1 1
#xt$config$table$is_response_transformed <- TRUE
res <- xt$get_Aggregator()
x <- res$medpolish()
#> Warning: You did not transform the intensities.medpolish works best with already variance stabilized intensities.Use LFQData$get_Transformer to transform the data :abundance
#> starting aggregation
towide <- tidy_to_wide_config(x$data, x$config, value = x$config$table$nr_children)
dd <- prolfqua::sim_lfq_data_protein_config()
#> creating sampleName from fileName column
#> completing cases
dd$config$table$nr_children
#> [1] "nr_peptides"
dd$data
#> # A tibble: 120 × 8
#> sample sampleName group_ isotopeLabel protein_Id abundance qValue nr_peptides
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 A_V1 A_V1 A light 0EfVhX~00… 20.1 0 3
#> 2 A_V1 A_V1 A light 7cbcrd~57… 22.0 0 1
#> 3 A_V1 A_V1 A light 9VUkAq~47… 19.8 0 1
#> 4 A_V1 A_V1 A light BEJI92~52… 21.2 0 2
#> 5 A_V1 A_V1 A light CGzoYe~21… 29.4 0 1
#> 6 A_V1 A_V1 A light DoWup2~58… NA NA NA
#> 7 A_V1 A_V1 A light Fl4JiV~86… 20.1 0 4
#> 8 A_V1 A_V1 A light HvIpHG~90… 21.7 0 2
#> 9 A_V1 A_V1 A light JcKVfU~96… 34.5 0 7
#> 10 A_V1 A_V1 A light SGIVBl~57… 23.9 0 6
#> # ℹ 110 more rows
xt <- tidy_to_wide_config(dd$data, dd$config, value = dd$config$table$nr_children)
xt$data
#> # A tibble: 10 × 14
#> protein_Id isotopeLabel A_V1 A_V2 A_V3 A_V4 B_V1 B_V2 B_V3 B_V4
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0EfVhX~0087 light 3 3 NA 3 3 3 3 3
#> 2 7cbcrd~5725 light 1 1 1 1 NA NA 1 NA
#> 3 9VUkAq~4703 light 1 1 1 1 1 1 1 1
#> 4 BEJI92~5282 light 2 NA 2 2 2 2 2 2
#> 5 CGzoYe~2147 light 1 1 1 1 1 1 1 1
#> 6 DoWup2~5896 light NA 1 1 1 1 1 NA 1
#> 7 Fl4JiV~8625 light 4 4 NA 4 4 4 4 4
#> 8 HvIpHG~9079 light 2 2 NA 2 2 2 2 2
#> 9 JcKVfU~9653 light 7 7 7 7 7 7 7 7
#> 10 SGIVBl~5782 light 6 6 6 6 6 6 NA 6
#> # ℹ 4 more variables: Ctrl_V1 <dbl>, Ctrl_V2 <dbl>, Ctrl_V3 <dbl>,
#> # Ctrl_V4 <dbl>