evex_download {OmnipathR} | R Documentation

## 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>

[Package OmnipathR version 3.2.0 Index]