remap_filtered {OmnipathR} | R Documentation

## Downloads TF-target interactions from ReMap

### Description

Downloads the ReMap TF-target interactions as processed by Garcia-Alonso et al. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6673718/#s1title) and filters them based on a score threshold, the top targets and whether the TF is included in the TF census (Vaquerizas et al. 2009). The code for filtering is adapted from DoRothEA, written by Christian Holland.

### Usage

    remap_filtered(score = 100, top_targets = 500, only_known_tfs = TRUE)

### Arguments

`score` | Numeric: a minimum score between 0 and 1000, records with lower scores will be excluded. If NULL no filtering performed.
`top_targets` | Numeric: the number of top scoring targets for each TF. Essentially the maximum number of targets per TF. If NULL the number of targets is not restricted.
`only_known_tfs` | Logical: whether to exclude TFs which are not in TF census.

### Value

Data frame with TF-target relationships.

### See Also

- `remap_tf_target_download`

- `remap_filtered`

- `tfcensus_download`

### Examples

    remap_interactions <- remap_filtered()
    nrow(remap_interactions)
    # [1] 145680

    remap_interactions <- remap_filtered(top_targets = 100)
    remap_interactions
    # # A tibble: 30,330 x 2
    #    source_genesymbol target_genesymbol
    #    <chr>             <chr>
    #  1 ADNP              ABCC1
    #  2 ADNP              ABT1
    #  3 ADNP              AC006076.1
    #  4 ADNP              AC007792.1
    #  5 ADNP              AC011288.2
    # # . with 30,320 more rows

[Package OmnipathR version 3.2.0 Index]