phenos_to_granges: Phenotypes to GenomicRanges

In neurogenomics/HPOExplorer: Analysis and Visualisation of the Human Phenotype Ontology

Phenotypes to GenomicRanges

Description

Convert a HPO phenotype dataframe generated by make_phenos_dataframe to a GRangesList split by HPO ID. The resulting object will contain genes (and gene metadata) for all genes associated with each phenotypes.

Usage

phenos_to_granges(
  phenos = NULL,
  phenotype_to_genes = load_phenotype_to_genes(),
  hpo = get_hpo(),
  keep_chr = c(seq(22), "X", "Y"),
  by = c("hpo_id", "disease_id"),
  gene_col = "intersection",
  split.field = "hpo_id",
  as_datatable = FALSE,
  allow.cartesian = FALSE,
  verbose = TRUE
)

Arguments

phenos	A data.table containing HPO IDs and other metadata.
phenotype_to_genes	Output of load_phenotype_to_genes mapping phenotypes to gene annotations.
hpo	Human Phenotype Ontology object, loaded from get_ontology.
keep_chr	Chromosomes to keep.
by	A vector of shared column names in x and y to merge on. This defaults to the shared key columns between the two tables. If y has no key columns, this defaults to the key of x.
gene_col	Name of the gene column.
split.field	A character string of a recognized column name in df that contains the grouping. This column defines how the rows of df are split and is typically a factor or character vector. When split.field is not provided the df will be split by the number of rows.
as_datatable	Return as a data.table.
allow.cartesian	See allow.cartesian in [.data.table.
verbose	Print messages.

Value

A GRangesList.

Examples

phenos <- make_phenos_dataframe(ancestor = "Neurodevelopmental delay")
grl <- phenos_to_granges(phenos = phenos)

neurogenomics/HPOExplorer documentation built on Aug. 24, 2024, 1:39 a.m.