remap_tf_target_download: Downloads TF-target interactions from ReMap

In saezlab/OmnipathR: OmniPath web service client and more

Downloads TF-target interactions from ReMap

Description

ReMap (http://remap.univ-amu.fr/) is a database of ChIP-Seq experiments. It provides raw and merged peaks and CRMs (cis regulatory motifs) with their associations to regulators (TFs). TF-target relationships can be derived as it is written in Garcia-Alonso et al. 2019: "For ChIP-seq, we downloaded the binding peaks from ReMap and scored the interactions between each TF and each gene according to the distance between the TFBSs and the genes’ transcription start sites. We evaluated different filtering strategies that consisted of selecting only the top-scoring 100, 200, 500, and 1000 target genes for each TF." (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6673718/#s1title). This function retrieves the full processed TF-target list from the data deposited in https://zenodo.org/record/3713238.

Usage

remap_tf_target_download()

Value

Data frame with TF-target relationships.

See Also

• remap_dorothea_download

• remap_filtered

Examples

## Not run: 
remap_interactions <- remap_tf_target_download()
remap_interactions
# # A tibble: 9,546,470 x 4
#    source_genesymbol target_genesymbol target_ensembl     score
#    <chr>             <chr>             <chr>              <dbl>
#  1 ADNP              PTPRS             ENSG00000105426.16  1000
#  2 AFF4              PRKCH             ENSG00000027075.14  1000
#  3 AHR               CTNND2            ENSG00000169862.18  1000
#  4 AR                PDE4D             ENSG00000113448.18  1000
#  5 ARID1A            PLEC              ENSG00000178209.14  1000
# # . with 9,546,460 more rows

## End(Not run)

saezlab/OmnipathR documentation built on Oct. 16, 2024, 11:49 a.m.