get_fantom5_enhancers_from_hgnc: Get the enhancers associated to certain genes from FANTOM5

In MCorentin/vargen: Fetching Variants Related to Phenotypes Using Public Databases

Get the enhancers associated to certain genes from FANTOM5

Description

from the FANTOM5 dataset, get the enhancers associated to the genes using the HGNC symbols, the association must pass the correlation threshold given by the user. Is used internally by get_fantom5_variants

Usage

get_fantom5_enhancers_from_hgnc(fantom_df, hgnc_symbols, corr_threshold = 0.25)

Arguments

fantom_df	the output of prepare_fantom
hgnc_symbols	vector of HUGO ids for the genes of interest
corr_threshold	the minimum correlation (z-score) to consider a enhancer/gene assocation valid (default: 0.25). A z-score greater than 0 represents an element greater than the mean, this means that this association has more correlation than random motifs.

Value

a subset of the FANTOM5 data.frame containing the information about the enhancers. The data.frame contains the following columns

• chr (chromosome)

• start (start of the enhancers)

• end (end of the enhancers)

• symbol (HGNC symbol of the gene associated to the enhancer)

• corr (correlation z-score from FANTOM5)

• fdr (False Discovery Rate)

MCorentin/vargen documentation built on Feb. 6, 2024, 2:32 p.m.