get_fantom5_variants: Get variants on the enhancers of the list of genes given as...

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

Get variants on the enhancers of the list of genes given as input

Description

FANTOM5 is used to get the enhancers of the genes, then the variants located on the enhancers are fetched with get_variants_from_locations It is also possible to specify a correlation threshold to limit the number of association to output (default: 0.25). The enhancer tss association file is based on hg19, so liftOver is needed.

Usage

get_fantom5_variants(
  fantom_df,
  omim_genes,
  corr_threshold = 0.25,
  hg19ToHg38.over.chain,
  verbose = FALSE
)

Arguments

fantom_df	the output of prepare_fantom
omim_genes	output from get_omim_genes
corr_threshold	the minimum correlation (z-score) to consider a enhancer/gene association 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.
hg19ToHg38.over.chain	the chain file to liftOver locations from hg19 to hg38.
verbose	if true, will print progress information (default: FALSE)

Value

a data.frame with information about the variants located on the enhancers. The data.frame will contain the following columns:

• chr (chromosome)

• pos (position of the variant)

• rsid (variant ID)

• ensembl_gene_id ("gene id" of the gene associated with the variant)

• hgnc_symbol ("hgnc symbol" of the gene associated with the variant)

• source (here the value will be "fantom5")

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