Filter interactions by extra attribute values
Arguments
- data
An interaction data frame with extra_attrs column.
- ...
Extra attribute names and values. The contents of the extra attribute name for each record will be checked against the values provided. The check by default is a set intersection: if any element is common between the user provided values and the values of the extra attribute for the record, the record will be matched. Alternatively, any value can be a custom function which accepts the value of the extra attribute and returns a single logical value. Finally, if the extra attribute name starts with a dot, the result of the check will be negated.
- na_ok
Logical: keep the records which do not have the extra attribute. Typically these are the records which are not from the resource providing the extra attribute.
Examples
cl <- import_post_translational_interactions(
resources = 'Cellinker',
fields = 'extra_attrs'
)
# Only cell adhesion interactions from Cellinker
filter_extra_attrs(cl, Cellinker_type = 'Cell adhesion')
#> # A tibble: 1,749 × 16
#> source target source_genesymbol target_genesymbol is_directed is_stimulation
#> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 O60674 P19235 JAK2 EPOR 1 1
#> 2 Q9Y219 P46531 JAG2 NOTCH1 1 1
#> 3 O00548 P46531 DLL1 NOTCH1 1 1
#> 4 P78504 P46531 JAG1 NOTCH1 1 1
#> 5 P04899 P48039 GNAI2 MTNR1A 1 0
#> 6 P42081 P10747 CD86 CD28 1 1
#> 7 P33681 P10747 CD80 CD28 1 1
#> 8 P04083 P25090 ANXA1 FPR2 1 1
#> 9 O43557 P36941 TNFSF14 LTBR 1 1
#> 10 Q06643 P36941 LTB LTBR 1 1
#> # ℹ 1,739 more rows
#> # ℹ 10 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
#> # consensus_stimulation <dbl>, consensus_inhibition <dbl>,
#> # extra_attrs <list>, sources <chr>, references <chr>, curation_effort <dbl>,
#> # n_references <int>, n_resources <int>
op <- import_omnipath_interactions(fields = 'extra_attrs')
# Any mechanism except phosphorylation
filter_extra_attrs(op, .SIGNOR_mechanism = 'phosphorylation')
#> # A tibble: 77,203 × 16
#> source target source_genesymbol target_genesymbol is_directed is_stimulation
#> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 P0DP23 P48995 CALM1 TRPC1 1 0
#> 2 P0DP25 P48995 CALM3 TRPC1 1 0
#> 3 P0DP24 P48995 CALM2 TRPC1 1 0
#> 4 Q03135 P48995 CAV1 TRPC1 1 1
#> 5 P14416 P48995 DRD2 TRPC1 1 1
#> 6 Q99750 P48995 MDFI TRPC1 1 0
#> 7 Q14571 P48995 ITPR2 TRPC1 1 1
#> 8 P29966 P48995 MARCKS TRPC1 1 0
#> 9 Q13255 P48995 GRM1 TRPC1 1 1
#> 10 Q13586 P48995 STIM1 TRPC1 1 1
#> # ℹ 77,193 more rows
#> # ℹ 10 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
#> # consensus_stimulation <dbl>, consensus_inhibition <dbl>,
#> # extra_attrs <list>, sources <chr>, references <chr>, curation_effort <dbl>,
#> # n_references <int>, n_resources <int>