evex_download {OmnipathR} | R Documentation |
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.
evex_download( min_confidence = NULL, remove_negatives = TRUE, top_confidence = NULL )
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. |
Data frame (tibble) with interactions.
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>