tidy_to_triple.RdConvert a tidy_omic object into a triple_omic object.
tidy_to_triple(tidy_omic)an object of class tidy_omic produced by
create_tidy_omic
The data table will be converted into features,
samples, and measurements tables using the design
to determine which variables belong in each table. The design
will be preserved as-is.
tidy_to_triple(brauer_2008_tidy)
#> $features
#> # A tibble: 500 × 4
#> name BP MF systematic_name
#> <chr> <chr> <chr> <chr>
#> 1 YOL029C biological process unknown mole… YOL029C
#> 2 SCW11 cytokinesis, completion of separation gluc… YGL028C
#> 3 YHR036W biological process unknown mole… YHR036W
#> 4 BGL2 cell wall organization and biogenesis gluc… YGR282C
#> 5 ACT1 cell wall organization and biogenesis* stru… YFL039C
#> 6 FKH1 pseudohyphal growth* tran… YIL131C
#> 7 HOC1 cell wall mannoprotein biosynthesis* tran… YJR075W
#> 8 CSN12 adaptation to pheromone during conjugation wit… mole… YJR084W
#> 9 YAL046C biological process unknown mole… YAL046C
#> 10 SLG1 cell wall organization and biogenesis* tran… YOR008C
#> # ℹ 490 more rows
#>
#> $samples
#> # A tibble: 36 × 3
#> sample nutrient DR
#> <chr> <chr> <dbl>
#> 1 G0.05 G 0.05
#> 2 G0.1 G 0.1
#> 3 G0.15 G 0.15
#> 4 G0.2 G 0.2
#> 5 G0.25 G 0.25
#> 6 G0.3 G 0.3
#> 7 N0.05 N 0.05
#> 8 N0.1 N 0.1
#> 9 N0.15 N 0.15
#> 10 N0.2 N 0.2
#> # ℹ 26 more rows
#>
#> $measurements
#> # A tibble: 18,000 × 3
#> name sample expression
#> <chr> <chr> <dbl>
#> 1 YOL029C G0.05 -0.22
#> 2 SCW11 G0.05 -0.67
#> 3 YHR036W G0.05 -0.91
#> 4 BGL2 G0.05 -0.08
#> 5 ACT1 G0.05 -0.04
#> 6 FKH1 G0.05 -0.57
#> 7 HOC1 G0.05 -0.42
#> 8 CSN12 G0.05 -0.49
#> 9 YAL046C G0.05 0.05
#> 10 SLG1 G0.05 -0.06
#> # ℹ 17,990 more rows
#>
#> $design
#> $design$features
#> # A tibble: 4 × 2
#> variable type
#> <chr> <chr>
#> 1 name feature_primary_key
#> 2 systematic_name character
#> 3 BP character
#> 4 MF character
#>
#> $design$samples
#> # A tibble: 3 × 2
#> variable type
#> <chr> <chr>
#> 1 sample sample_primary_key
#> 2 nutrient character
#> 3 DR numeric
#>
#> $design$measurements
#> # A tibble: 3 × 2
#> variable type
#> <chr> <chr>
#> 1 name feature_primary_key
#> 2 sample sample_primary_key
#> 3 expression numeric
#>
#> $design$feature_pk
#> [1] "name"
#>
#> $design$sample_pk
#> [1] "sample"
#>
#>
#> attr(,"class")
#> [1] "triple_omic" "tomic" "general"