## ----message=FALSE, warning=FALSE--------------------------------------------------------------------------- library(OmnipathR) ## ----load-interactions-------------------------------------------------------------------------------------- i <- import_post_translational_interactions(fields = 'extra_attrs') dplyr::select(i, source_genesymbol, target_genesymbol, extra_attrs) ## ----list-extra-attrs--------------------------------------------------------------------------------------- extra_attrs(i) ## ----extra-attr-values-------------------------------------------------------------------------------------- extra_attr_values(i, SIGNOR_mechanism) ## ----to-cols------------------------------------------------------------------------------------------------ i0 <- extra_attrs_to_cols( i, si_mechanism = SIGNOR_mechanism, ma_mechanism = Macrophage_type, keep_empty = FALSE ) dplyr::select( i0, source_genesymbol, target_genesymbol, si_mechanism, ma_mechanism ) ## ----single-value-vector------------------------------------------------------------------------------------ dplyr::pull(i0, si_mechanism)[[7]] ## ----to-cols-flatten---------------------------------------------------------------------------------------- i1 <- extra_attrs_to_cols( i, si_mechanism = SIGNOR_mechanism, ma_mechanism = Macrophage_type, keep_empty = FALSE, flatten = TRUE ) dplyr::select( i1, source_genesymbol, target_genesymbol, si_mechanism, ma_mechanism ) ## ----with-attrs-1------------------------------------------------------------------------------------------- nrow(with_extra_attrs(i, SIGNOR_mechanism)) ## ----with-attrs-2------------------------------------------------------------------------------------------- nrow(with_extra_attrs(i, SIGNOR_mechanism, CA1_effect, Li2012_mechanism)) ## ----signor-phos-1------------------------------------------------------------------------------------------ phos <- c('phosphorylation', 'Phosphorylation') si_phos <- filter_extra_attrs(i, SIGNOR_mechanism = phos) dplyr::select(si_phos, source_genesymbol, target_genesymbol) ## ----search-attr-------------------------------------------------------------------------------------------- keys <- extra_attrs(i) keys_ubi <- purrr::keep( keys, function(k){ any(stringr::str_detect(extra_attr_values(i, !!k), 'biqu')) } ) keys_ubi ## ----search-values------------------------------------------------------------------------------------------ ubi <- rlang::set_names( purrr::map( keys_ubi, function(k){ stringr::str_subset(extra_attr_values(i, !!k), 'biqu') } ), keys_ubi ) ubi ## ----filter-ubi--------------------------------------------------------------------------------------------- ubi_kws <- c('ubiquitination', 'Ubiquitination') i_ubi <- dplyr::distinct( dplyr::bind_rows( purrr::map( keys_ubi, function(k){ filter_extra_attrs(i, !!k := ubi_kws, na_ok = FALSE) } ) ) ) dplyr::select(i_ubi, source_genesymbol, target_genesymbol) ## ----count-e3----------------------------------------------------------------------------------------------- length(unique(i_ubi$source_genesymbol)) ## ----match-e3----------------------------------------------------------------------------------------------- uniprot_kws <- import_omnipath_annotations( resources = 'UniProt_keyword', entity_type = 'protein', wide = TRUE ) e3_ligases <- dplyr::pull( dplyr::filter(uniprot_kws, keyword == 'Ubl conjugation'), genesymbol ) length(e3_ligases) length(intersect(unique(i_ubi$source_genesymbol), e3_ligases)) length(setdiff(unique(i_ubi$source_genesymbol), e3_ligases)) ## ----ubi-es------------------------------------------------------------------------------------------------- es_ubi <- import_omnipath_enzsub(types = 'ubiquitination') es_ubi ## ----match-es----------------------------------------------------------------------------------------------- es_i_ubi <- dplyr::inner_join( es_ubi, i_ubi, by = c( 'enzyme_genesymbol' = 'source_genesymbol', 'substrate_genesymbol' = 'target_genesymbol' ) ) nrow(dplyr::distinct(dplyr::select(es_i_ubi, enzyme, substrate, residue_offset))) ## ----session------------------------------------------------------------------------------------------------ sessionInfo()