BioPlex provides four interaction datasets: version 1.0, 2.0, 3.0 and HCT116 version 1.0. This function downloads all of them, merges them to one data frame, removes the duplicates (based on unique pairs of UniProt IDs) and separates the isoform numbers from the UniProt IDs. More details at https://bioplex.hms.harvard.edu/interactions.php.
Arguments
- unique
Logical. Collapse the duplicate interactions into single rows or keep them as they are. In case of merging duplicate records the maximum p value will be choosen for each record.
Examples
bioplex_interactions <- bioplex_all()
bioplex_interactions
#> # A tibble: 195,538 × 11
#> UniprotA IsoformA UniprotB IsoformB GeneA GeneB SymbolA SymbolB p_wrong
#> <chr> <int> <chr> <int> <dbl> <dbl> <chr> <chr> <dbl>
#> 1 A0AV02 2 Q5K4L6 NA 84561 11000 SLC12A8 SLC27A3 2.11e- 8
#> 2 A0AV02 2 Q8N5V2 NA 84561 25791 SLC12A8 NGEF 1.23e- 9
#> 3 A0AV02 2 Q9H6S3 NA 84561 64787 SLC12A8 EPS8L2 1.89e-10
#> 4 A0AV96 2 O00425 2 54502 10643 RBM47 IGF2BP3 5.57e-14
#> 5 A0AV96 2 O00443 NA 54502 5286 RBM47 PIK3C2A 1.55e-12
#> 6 A0AV96 2 O43426 NA 54502 8867 RBM47 SYNJ1 1.62e- 2
#> 7 A0AV96 2 O75127 NA 54502 26024 RBM47 PTCD1 5.28e-12
#> 8 A0AV96 2 O95208 2 54502 22905 RBM47 EPN2 1.34e- 9
#> 9 A0AV96 2 O95900 NA 54502 26995 RBM47 TRUB2 1.41e-10
#> 10 A0AV96 2 P07910 2 54502 3183 RBM47 HNRNPC 6.25e-13
#> # ℹ 195,528 more rows
#> # ℹ 2 more variables: p_no_interaction <dbl>, p_interaction <dbl>
# # A tibble: 195,538 x 11
# UniprotA IsoformA UniprotB IsoformB GeneA GeneB SymbolA SymbolB
# <chr> <int> <chr> <int> <dbl> <dbl> <chr> <chr>
# 1 A0AV02 2 Q5K4L6 NA 84561 11000 SLC12A8 SLC27A3
# 2 A0AV02 2 Q8N5V2 NA 84561 25791 SLC12A8 NGEF
# 3 A0AV02 2 Q9H6S3 NA 84561 64787 SLC12A8 EPS8L2
# 4 A0AV96 2 O00425 2 54502 10643 RBM47 IGF2BP3
# 5 A0AV96 2 O00443 NA 54502 5286 RBM47 PIK3C2A
# 6 A0AV96 2 O43426 NA 54502 8867 RBM47 SYNJ1
# 7 A0AV96 2 O75127 NA 54502 26024 RBM47 PTCD1
# 8 A0AV96 2 O95208 2 54502 22905 RBM47 EPN2
# 9 A0AV96 2 O95900 NA 54502 26995 RBM47 TRUB2
# 10 A0AV96 2 P07910 2 54502 3183 RBM47 HNRNPC
# # . with 195,528 more rows, and 3 more variables: p_wrong <dbl>,
# # p_no_interaction <dbl>, p_interaction <dbl>