Type: Package
Title: Gene Set Enrichment Analysis in R
Version: 1.5
Date: 2024-02-20
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Description: R-interface to C++ implementation of the rank/score permutation based GSEA test (Subramanian et al 2005 <doi:10.1073/pnas.0506580102>).
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Imports: Rcpp (≥ 0.11.2), ontologyIndex (≥ 2.0)
LinkingTo: Rcpp
Depends: R (≥ 3.0.0)
Suggests: markdown, knitr
VignetteBuilder: knitr
RoxygenNote: 7.2.1
NeedsCompilation: yes
Packaged: 2024-02-20 21:24:13 UTC; dg
Repository: CRAN
Date/Publication: 2024-02-20 21:40:02 UTC

Gene Set Enrichment Analysis in R

Description

R-interface to C++ implementation of the rank/score based GSEA test described by Subramanian et al 2005.

Author(s)

Daniel Greene <dg333@cam.ac.uk>

Maintainer: Daniel Greene <dg333@cam.ac.uk>

References

Subramanian, A, Tamayo, P, Mootha, VK, Mukherjee, S, Ebert, BL, Gillette, MA, Paulovich, A, Pomeroy, SL, Golub, TR, Lander, ES, Mesirov, JP (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U.S.A., 102, 43:15545-50, doi: 10.1073/pnas.0506580102.

Ashburner et al. Gene ontology: tool for the unification of biology (2000) Nat Genet 25(1):25-9

GO term gene sets

Description

List of gene sets annotated by each GO term

Format

List of character vectors of genes per GO term, and named by term ID.

Details

Based on gene-GO term annotations downloaded from geneontology.org. Only contains gene sets for terms with up to 500 genes.

Create list of gene sets defined by GO term annotation

Description

Note, this function takes several minutes to execute.

Usage

get_GO_gene_sets(
  GO_annotation_file,
  GO_file = "http://purl.obolibrary.org/obo/go.obo",
  min_genes = 15,
  max_genes = 500,
  verbose = TRUE
)

Arguments

GO_annotation_file

File path of annotation file, which should contain a column of genes and a column of terms. Can be downloaded from at http://geneontology.org/gene-associations/gene_association.goa_human.gz.

GO_file

File path of gene ontology.

min_genes

Minimum number of genes in gene sets.

max_genes

Maximum number of genes in gene sets.

verbose

Print progress.

Value

List of character vectors of term IDs.

Create list of gene sets defined by ontological annotation

Description

Create list of gene sets defined by ontological annotation

Usage

get_ontological_gene_sets(ontology, gene, term, min_genes = 1, max_genes = 500)

Arguments

ontology

ontology_index object.

gene

Character vector of genes.

term

Character vector of term IDs annotated to corresponding genes.

min_genes

Minimum number of genes in gene sets.

max_genes

Maximum number of genes in gene sets.

Value

List of character vectors of term IDs.

Gene set enrichment test

Description

Gene set enrichment test

Usage

gset(
  S,
  N = NULL,
  r = NULL,
  p = 1,
  min_its = 200,
  max_its = 1e+05,
  significance_threshold = 0.05,
  log_dismiss = -10,
  raw_score = FALSE
)

Arguments

S

Ranks of gene set

N

Integer value. Only required if r is not specified.

r

Rank/correlation scores. If S is character, then r must be named by gene or be a character vector of the gene names in rank order (necessarily containing S).

p

Weighting of ranking/correlations, see Subramanian et. al 2005.

min_its

Minimum number of null permutations to compare.

max_its

Maximum number of null permutations to compare.

significance_threshold

Maximum p-value of significant result.

log_dismiss

Threshold log probability of returning a significant result, below which function returns current p-value.

raw_score

Logical value determining whether to return the raw value of the gene set enrichment score.

Value

Numeric value - p-value of enrichment.

Examples

gset(S=1:5 * 2, N=1000)
gset(S=letters[1:3], r=letters)