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.
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.
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 ¹general_event_id, ²source_entrezgene_id,
#> # ³target_entrezgene_id, ⁴confidence, ⁵negation, ⁶speculation, ⁷coarse_type,
#> # ⁸coarse_polarity, ⁹refined_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>