pivot_annotations: Converts annotation tables to a wide format
In saezlab/OmnipathR: OmniPath web service client and more

pivot_annotations

R Documentation

Converts annotation tables to a wide format

Description

Use this method to reconstitute the annotation tables into the format of the original resources. With the 'wide=TRUE' option annotations applies this function to the downloaded data.

Usage

pivot_annotations(annotations)

Arguments

annotations

A data frame of annotations downloaded from the OmniPath web service by annotations.

Value

A wide format data frame (tibble) if the provided data contains annotations from one resource, otherwise a list of wide format tibbles.

Examples

# single resource: the result is a data frame
disgenet <- annotations(resources = "DisGeNet")
disgenet <- pivot_annotations(disgenet)
disgenet
# # A tibble: 126,588 × 11
#    uniprot genesymbol entity_type disease      type  score   dsi   dpi
#    <chr>   <chr>      <chr>       <chr>        <chr> <dbl> <dbl> <dbl>
#  1 P04217  A1BG       protein     Schizophren. dise.  0.3  0.7   0.538
#  2 P04217  A1BG       protein     Hepatomegaly phen.  0.3  0.7   0.538
#  3 P01023  A2M        protein     Fibrosis, L. dise.  0.3  0.529 0.769
#  4 P01023  A2M        protein     Acute kidne. dise.  0.3  0.529 0.769
#  5 P01023  A2M        protein     Mental Depr. dise.  0.3  0.529 0.769
# # . with 126,583 more rows, and 3 more variables: nof_pmids <dbl>,
# #   nof_snps <dbl>, source <chr>

# multiple resources: the result is a list
annot_long <- annotations(
    resources = c("DisGeNet", "SignaLink_function", "DGIdb", "kinase.com")
)
annot_wide <- pivot_annotations(annot_long)
names(annot_wide)
# [1] "DGIdb"              "DisGeNet"           "kinase.com"
# [4] "SignaLink_function"
annot_wide$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

saezlab/OmnipathR documentation built on Oct. 16, 2024, 11:49 a.m.