remap_dorothea_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 returns the top TF-target relationships as used in DoRothEA: https://github.com/saezlab/dorothea/blob/master/inst/scripts/02_chip_seq.R).

Usage

remap_dorothea_download()

Value

Data frame with TF-target relationships.

See Also

remap_tf_target_download

Examples

remap_interactions <- remap_dorothea_download()
remap_interactions
# # A tibble: 136,988 x 2
#    tf    target
#    <chr> <chr>
#  1 ADNP  ABCC1
#  2 ADNP  ABCC6
#  3 ADNP  ABHD5
#  4 ADNP  ABT1
#  5 ADNP  AC002066.1
# # . with 136,978 more rows

saezlab/OmnipathR documentation built on May 3, 2024, 5:32 a.m.