load the transcription factors from DOROTHEA package and converts
gene symbols to EntrezID using org.Hs.eg.db
Usage
load_tf_regulon_dorothea(confidence = c("A", "B", "C"))
Arguments
- 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()
#> # A tibble: 13,223 × 3
#> tf target sign
#> <chr> <chr> <dbl>
#> 1 AHR CYP1A1 1
#> 2 AHR CYP1A2 1
#> 3 AHR CYP1B1 1
#> 4 AHR FOS 1
#> 5 AHR MYC 1
#> 6 AHR UGT1A6 1
#> 7 AHR ASAP1 1
#> 8 AHR ERG 1
#> 9 AHR VGLL4 1
#> 10 AHR ARHGAP15 1
#> # ℹ 13,213 more rows
