load the transcription factors from DOROTHEA package and converts gene symbols to EntrezID using org.Hs.eg.db

load_tf_regulon_dorothea(toEntrez = TRUE, confidence = c("A", "B", "C"))

Arguments

toEntrez

if TRUE (default), converts gene symbols to EntrezID

confidence

strong vector (by default: c("A","B","C")). Subset of {A, B, C, D, E}. See the `dorothea` for the meaning of confidence levels. package for further details.

Value

returns a PKN of a form of a data table. Each row is an interaction. Columns names are:

- `tf` transcription factor - `confidence` class of confidence - `target` target gene - `sign` indicates if interaction is up (1) or down-regulation (-1).

Examples

load_tf_regulon_dorothea()
#> 'select()' returned 1:1 mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> # A tibble: 13,185 x 3 #> tf sign target #> <chr> <dbl> <chr> #> 1 X196 1 X1543 #> 2 X196 1 X1544 #> 3 X196 1 X1545 #> 4 X196 1 X2353 #> 5 X196 1 X4609 #> 6 X196 1 X54578 #> 7 X196 1 X50807 #> 8 X196 1 X2078 #> 9 X196 1 X9686 #> 10 X196 1 X55843 #> # … with 13,175 more rows