make_gsc_from_ids: Create a gene set collection from a set of arbitrary IDs.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Create a gene set collection from a set of arbitrary IDs.

Description

This function attempts to simplify the creation of a gsva compatible GeneSet. Some important caveats when working with gsva, notably the gene IDs we use are not usually compatible with the gene IDs used by gsva, thus the primary logic in this function is intended to bridge these IDs.

Usage

make_gsc_from_ids(
  first_ids,
  second_ids = NULL,
  annotation_name = "org.Hs.eg.db",
  researcher_name = "elsayed",
  study_name = "macrophage",
  category_name = "infection",
  phenotype_name = NULL,
  identifier_type = "entrez",
  organism = NULL,
  pair_names = "up",
  current_id = "ENSEMBL",
  required_id = "ENTREZID",
  min_gmt_genes = 10
)

Arguments

first_ids	The required IDs for a single set.
second_ids	Potentially null optionally used for a second, presumably contrasting set.
annotation_name	Orgdb annotation, used to translate IDs to the required type.
researcher_name	Prefix of the name for the generated set(s).
study_name	Second element in the name of the generated set(s).
category_name	Third element in the name of the generated set(s).
phenotype_name	Optional phenotype data for the generated set(s).
identifier_type	ID type to use in the gene set.
organism	Set the organism for the gsc object.
pair_names	The suffix of the generated set(s).
current_id	What type of ID is the data currently using?
required_id	What type of ID should the use?
min_gmt_genes	Minimum number of genes in the set for consideration.

Value

Small list comprised of the created gene set collection(s).

See Also

[GSEABase]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.