remap_filtered | R Documentation |
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.
remap_filtered(score = 100, top_targets = 500, only_known_tfs = TRUE)
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. |
Data frame with TF-target relationships.
remap_tf_target_download
remap_filtered
tfcensus_download
## Not run:
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
## End(Not run)
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