triple_to_tidy.RdConvert a triple_omic object into a tidy_omic oobject.
triple_to_tidy(triple_omic)an object of class triple_omic produced by
create_triple_omic
Features, samples and measurements will be merged into a single data
table, and the design will be preserved as-is.
library(dplyr)
measurement_df <- tidyr::expand_grid(
feature_id = 1:10,
sample_id = LETTERS[1:5]
) %>%
dplyr::mutate(value = rnorm(n()))
feature_df <- tibble(
feature_id = 1:10,
feature_group = rep(c("a", "b"), each = 5)
)
sample_df <- tibble(
sample_id = LETTERS[1:5],
sample_group = c("a", "a", "b", "b", "b")
)
triple_omic <- create_triple_omic(
measurement_df, feature_df, sample_df,
"feature_id", "sample_id"
)
triple_to_tidy(triple_omic)
#> $data
#> # A tibble: 50 × 5
#> feature_id feature_group sample_id sample_group value
#> <int> <chr> <chr> <chr> <dbl>
#> 1 1 a A a -0.669
#> 2 1 a B a 0.0900
#> 3 1 a C b -0.331
#> 4 1 a D b -0.514
#> 5 1 a E b -0.907
#> 6 2 a A a 0.241
#> 7 2 a B a -0.478
#> 8 2 a C b -2.46
#> 9 2 a D b -1.42
#> 10 2 a E b 0.467
#> # ℹ 40 more rows
#>
#> $design
#> $design$features
#> # A tibble: 2 × 2
#> variable type
#> <chr> <chr>
#> 1 feature_id feature_primary_key
#> 2 feature_group character
#>
#> $design$samples
#> # A tibble: 2 × 2
#> variable type
#> <chr> <chr>
#> 1 sample_id sample_primary_key
#> 2 sample_group character
#>
#> $design$measurements
#> # A tibble: 3 × 2
#> variable type
#> <chr> <chr>
#> 1 feature_id feature_primary_key
#> 2 sample_id sample_primary_key
#> 3 value numeric
#>
#> $design$feature_pk
#> [1] "feature_id"
#>
#> $design$sample_pk
#> [1] "sample_id"
#>
#>
#> attr(,"class")
#> [1] "tidy_omic" "tomic" "general"