consensuspathdb_download: Retrieves the ConsensusPathDB network

In saezlab/OmnipathR: OmniPath web service client and more

Retrieves the ConsensusPathDB network

Description

Compiles a table of binary interactions from ConsensusPathDB (http://cpdb.molgen.mpg.de/) and translates the UniProtKB ACs to Gene Symbols.

Usage

consensuspathdb_download(complex_max_size = 4, min_score = 0.9)

Arguments

complex_max_size

Numeric: do not expand complexes with a higher number of elements than this. ConsensusPathDB does not contain conventional interactions but lists of participants, which might be members of complexes. Some records include dozens of participants and expanding them to binary interactions result thousands, sometimes hundreds of thousands of interactions from one single record. At the end, this process consumes >10GB of memory and results rather unusable data, hence it is recommended to limit the complex sizes at some low number.

min_score

Numeric: each record in ConsensusPathDB comes with a confidence score, expressing the amount of evidences. The default value, a minimum score of 0.9 retains approx. the top 30 percent of the interactions.

Value

Data frame (tibble) with interactions.

Examples

## Not run: 
cpdb_data <- consensuspathdb_download(
    complex_max_size = 1,
    min_score = .99
)
nrow(cpdb_data)
# [1] 252302
colnames(cpdb_data)
# [1] "databases"  "references" "uniprot_a"    "confidence"   "record_id"
# [6] "uniprot_b"  "in_complex" "genesymbol_a" "genesymbol_b"
cpdb_data
# # A tibble: 252,302 x 9
#    databases references uniprot_a confidence record_id uniprot_b in_com
#    <chr>     <chr>      <chr>          <dbl>     <int> <chr>     <lgl>
#  1 Reactome  NA         SUMF2_HU.      1             1 SUMF1_HU. TRUE
#  2 Reactome  NA         SUMF1_HU.      1             1 SUMF2_HU. TRUE
#  3 DIP,Reac. 22210847,. STIM1_HU.      0.998         2 TRPC1_HU. TRUE
#  4 DIP,Reac. 22210847,. TRPC1_HU.      0.998         2 STIM1_HU. TRUE
# # . with 252,292 more rows, and 2 more variables: genesymbol_a <chr>,
# #   genesymbol_b <chr

## End(Not run)

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