| 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