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Interactions from the EVEX database

Source: R/evex.R
evex_download.Rd

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 × 13
#>    general_eve…¹ sourc…² targe…³ confi…⁴ negat…⁵ specu…⁶ coars…⁷ coars…⁸ refin…⁹
#>            <dbl> <chr>   <chr>     <dbl>   <dbl>   <dbl> <chr>   <chr>   <chr>  
#>  1            98 8651    6774     -1.45        0       0 Regula… Unspec… Regula…
#>  2           100 8431    6774     -1.45        0       0 Regula… Unspec… Regula…
#>  3           205 6261    6263      0.370       0       0 Binding Neutral Binding
#>  4           435 1044    1045     -1.09        0       0 Regula… Positi… Regula…
#>  5           440 1045    1044     -1.09        0       0 Regula… Positi… Regula…
#>  6           507 3596    952      -1.67        0       0 Regula… Unspec… Regula…
#>  7           559 5592    5329     -0.326       0       0 Regula… Unspec… Regula…
#>  8           575 85004   2255     -1.31        0       0 Regula… Negati… Regula…
#>  9           657 2321    7422     -1.32        0       0 Regula… Unspec… Regula…
#> 10           664 2321    7422     -0.544       0       1 Regula… Unspec… Regula…
#> # … with 368,287 more rows, 4 more variables: refined_polarity <chr>,
#> #   source_genesymbol <chr>, target_genesymbol <chr>, references <chr>, and
#> #   abbreviated variable names ¹​general_event_id, ²​source_entrezgene_id,
#> #   ³​target_entrezgene_id, ⁴​confidence, ⁵​negation, ⁶​speculation, ⁷​coarse_type,
#> #   ⁸​coarse_polarity, ⁹​refined_type
# # 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>