test_gene_enrichment {tidybulk} | R Documentation |
test_gene_enrichment() takes as imput a 'tbl' formatted as | <SAMPLE> | <ENSEMBL_ID> | <COUNT> | <...> | and returns a 'tbl' with the additional transcript symbol column
test_gene_enrichment( .data, .formula, .sample = NULL, .entrez, .abundance = NULL, .contrasts = NULL, species, cores = 10 ) ## S4 method for signature 'spec_tbl_df' test_gene_enrichment( .data, .formula, .sample = NULL, .entrez, .abundance = NULL, .contrasts = NULL, species, cores = 10 ) ## S4 method for signature 'tbl_df' test_gene_enrichment( .data, .formula, .sample = NULL, .entrez, .abundance = NULL, .contrasts = NULL, species, cores = 10 ) ## S4 method for signature 'tidybulk' test_gene_enrichment( .data, .formula, .sample = NULL, .entrez, .abundance = NULL, .contrasts = NULL, 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 ID of the transcripts/genes |
.abundance |
The name of the transcript/gene abundance column |
.contrasts |
= NULL, |
species |
A character. For example, human or mouse |
cores |
An integer. The number of cores available |
This wrapper execute gene enrichment analyses of the dataset
A 'tbl' object
A 'tbl' object
A 'tbl' object
A 'tbl' object
## Not run: df_entrez = symbol_to_entrez(tidybulk::counts_mini, .transcript = transcript, .sample = sample) df_entrez = aggregate_duplicates(df_entrez, aggregation_function = sum, .sample = sample, .transcript = entrez, .abundance = count) library("EGSEA") test_gene_enrichment( df_entrez, ~ condition, .sample = sample, .entrez = entrez, .abundance = count, species="human", cores = 1 ) ## End(Not run)