make_gsc_from_pairwise: 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! To that end, this function uses extract_significant_genes() in order to gather sets of genes deemed 'significant'. It then passes these sets to make_gsc_from_ids().

Usage

make_gsc_from_pairwise(
  pairwise,
  according_to = "deseq",
  annotation_name = "org.Hs.eg.db",
  pair_names = c("ups", "downs"),
  category_name = "infection",
  phenotype_name = "parasite",
  set_name = "elsayed_macrophage",
  color = TRUE,
  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 database for the data.
pair_names	Describe the contrasts of the GSC: up vs. down, high vs. low, etc.
category_name	What category does the GSC describe?
phenotype_name	When making color sets, use this phenotype name.
set_name	A name for the created gene set.
color	Make a colorSet?
current_id	Usually we use ensembl IDs, but that does not _need_ to be the case.
required_id	gsva uses entrezids by default.
...	Extra arguments for extract_significant_genes().

Value

List containing 3 GSCs, one containing both the ups/downs called 'colored', one of the ups, and one of the downs.

See Also

[combine_de_tables()] [extract_significant_genes()] [make_gsc_from_ids()] [GSEABase]

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