test_gene_enrichment_bulk_EGSEA {tidybulk} | R Documentation |
Get gene enrichment analyses using EGSEA
test_gene_enrichment_bulk_EGSEA( .data, .formula, .sample = NULL, .entrez, .abundance = NULL, .contrasts = NULL, methods, gene_sets, species, cores = 10 )
.data |
A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | |
.formula |
A formula with no response variable, representing the desired linear model |
.sample |
The name of the sample column |
.entrez |
The ENTREZ code of the transcripts/genes |
.abundance |
The name of the transcript/gene abundance column |
.contrasts |
A character vector. See edgeR makeContrasts specification for the parameter 'contrasts'. If contrasts are not present the first covariate is the one the model is tested against (e.g., ~ factor_of_interest) |
methods |
A character vector. One or 3 or more methods to use in the testing (currently EGSEA errors if 2 are used). Type EGSEA::egsea.base() to see the supported GSE methods. |
gene_sets |
A character vector or a list. It can take one or more of the following built-in collections as a character vector: c("h", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "kegg_disease", "kegg_metabolism", "kegg_signaling"), to be used with EGSEA buildIdx. c1 is human specific. Alternatively, a list of user-supplied gene sets can be provided, to be used with EGSEA buildCustomIdx. In that case, each gene set is a character vector of Entrez IDs and the names of the list are the gene set names. |
species |
A character. It can be human, mouse or rat. |
cores |
An integer. The number of cores available |
A tibble with edgeR results