evex_download: Interactions from the EVEX database

In saezlab/OmnipathR: OmniPath web service client and more

Interactions from the EVEX database

Description

Downloads interactions from EVEX, a versatile text mining resource (http://evexdb.org). Translates the Entrez Gene IDs to Gene Symbols and combines the interactions and references into a single data frame.

Usage

evex_download(
    min_confidence = NULL,
    remove_negatives = TRUE,
    top_confidence = NULL
)

Arguments

min_confidence	Numeric: a threshold for confidence scores. EVEX confidence scores span roughly from -3 to 3. By providing a numeric value in this range the lower confidence interactions can be removed. If NULL no filtering performed.
remove_negatives	Logical: remove the records with the "negation" attribute set.
top_confidence	Confidence cutoff as quantile (a number between 0 and 1). If NULL no filtering performed.

Value

Data frame (tibble) with interactions.

Examples

evex_interactions <- evex_download()
evex_interactions
# # A tibble: 368,297 x 13
#   general_event_id source_entrezge. target_entrezge. confidence negation
#               <dbl> <chr>            <chr>                 <dbl>    <dbl>
# 1               98 8651             6774                 -1.45         0
# 2              100 8431             6774                 -1.45         0
# 3              205 6261             6263                  0.370        0
# 4              435 1044             1045                 -1.09         0
# . with 368,287 more rows, and 8 more variables: speculation <dbl>,
#   coarse_type <chr>, coarse_polarity <chr>, refined_type <chr>,
#   refined_polarity <chr>, source_genesymbol <chr>,
#   target_genesymbol <chr>, references <chr>

saezlab/OmnipathR documentation built on Nov. 10, 2024, 11:02 p.m.