make_gsc_from_abundant: Given a pairwise result, make a gene set collection.

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

Given a pairwise result, make a gene set collection.

Description

If I want to play with gsva and friends, then I need GeneSetCollections! Much like make_gsc_from_significant(), this function extract the genes deemed 'abundant' and generates gene sets accordingly.

Usage

make_gsc_from_abundant(
  pairwise,
  according_to = "deseq",
  annotation_name = "org.Hs.eg.db",
  researcher_name = "elsayed",
  study_name = "macrophage",
  category_name = "infection",
  phenotype_name = NULL,
  pair_names = "high",
  current_id = "ENSEMBL",
  required_id = "ENTREZID",
  ...
)

Arguments

pairwise	A pairwise result, or combined de result, or extracted genes.
according_to	When getting significant genes, use this method.
annotation_name	Name of the annotation dataset.
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).
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?
...	Extra arguments for extract_abundant_genes().

Value

List containing 3 GSCs, one containing both the highs/lows called 'colored', one of the highs, and one of the lows.

See Also

[extract_abundant_genes()] [make_gsc_from_ids()] [GSEABase]

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