pivot_annotations {OmnipathR} | R Documentation |
Use this method to reconstitute the annotation tables into the format of
the original resources. With the 'wide=TRUE' option
import_omnipath_annotations
applies this function to the
downloaded data.
pivot_annotations(annotations)
annotations |
A data frame of annotations downloaded from the
OmniPath web service by |
A wide format data frame (tibble) if the provided data contains annotations from one resource, otherwise a list of wide format tibbles.
# single resource: the result is a data frame disgenet <- import_omnipath_annotations(resources = 'DisGeNet') disgenet <- pivot_annotations(disgenet) disgenet # # A tibble: 119,551 x 10 # uniprot genesymbol entity_type disease score dsi dpi nof_pmids # <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> # 1 P04217 A1BG protein Schizo… 0.3 0.857 0.172 1 # 2 P04217 A1BG protein Hepato… 0.3 0.857 0.172 1 # 3 P01023 A2M protein alpha-… 0.31 0.564 0.724 0 # 4 P01023 A2M protein Fibros… 0.3 0.564 0.724 1 # 5 P01023 A2M protein Hepato… 0.3 0.564 0.724 1 # # . with 119,541 more rows, and 2 more variables: nof_snps <chr>, # # source <chr> # multiple resources: the result is a list annotations <- import_omnipath_annotations( resources = c('DisGeNet', 'SignaLink_function', 'DGIdb', 'kinase.com') ) annotations <- pivot_annotations(annotations) names(annotations) # [1] "DGIdb" "DisGeNet" "kinase.com" # [4] "SignaLink_function" annotations$kinase.com # # A tibble: 825 x 6 # uniprot genesymbol entity_type group family subfamily # <chr> <chr> <chr> <chr> <chr> <chr> # 1 P31749 AKT1 protein AGC Akt NA # 2 P31751 AKT2 protein AGC Akt NA # 3 Q9Y243 AKT3 protein AGC Akt NA # 4 O14578 CIT protein AGC DMPK CRIK # 5 Q09013 DMPK protein AGC DMPK GEK # # . with 815 more rows