Title: | Gene Set Enrichment Analysis in R |
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Description: | R-interface to C++ implementation of the rank/score permutation based GSEA test (Subramanian et al 2005 <doi: 10.1073/pnas.0506580102>). |
Authors: | Daniel Greene |
Maintainer: | Daniel Greene <[email protected]> |
License: | GPL (>= 2) |
Version: | 1.5 |
Built: | 2025-02-15 02:38:11 UTC |
Source: | https://github.com/cran/gsEasy |
R-interface to C++ implementation of the rank/score based GSEA test described by Subramanian et al 2005.
Daniel Greene <[email protected]>
Maintainer: Daniel Greene <[email protected]>
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
Note, this function takes several minutes to execute.
get_GO_gene_sets( GO_annotation_file, GO_file = "http://purl.obolibrary.org/obo/go.obo", min_genes = 15, max_genes = 500, verbose = TRUE )
get_GO_gene_sets( GO_annotation_file, GO_file = "http://purl.obolibrary.org/obo/go.obo", min_genes = 15, max_genes = 500, verbose = TRUE )
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. |
List of character vectors of term IDs.
Create list of gene sets defined by ontological annotation
get_ontological_gene_sets(ontology, gene, term, min_genes = 1, max_genes = 500)
get_ontological_gene_sets(ontology, gene, term, min_genes = 1, max_genes = 500)
ontology |
|
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. |
List of character vectors of term IDs.
List of gene sets annotated by each GO term
List of character vectors of genes per GO term, and named by term ID.
Based on gene-GO term annotations downloaded from geneontology.org
. Only contains gene sets for terms with up to 500 genes.
Gene set enrichment test
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 )
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 )
S |
Ranks of gene set |
N |
Integer value. Only required if |
r |
Rank/correlation scores. If |
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. |
Numeric value - p-value of enrichment.
gset(S=1:5 * 2, N=1000) gset(S=letters[1:3], r=letters)
gset(S=1:5 * 2, N=1000) gset(S=letters[1:3], r=letters)