annotation_enrichment_analysis | R Documentation |
Perform enrichment analysis using a hypergeometric test for protein annotations stored in a formatted data.frame
annotation_enrichment_analysis(
df,
sep_split = "|",
sep = NULL,
idx_subset,
annotation_selected = names(df)[2],
col_names = names(df)[1],
two_sided = FALSE,
updateProgress = NULL,
showProgress = TRUE,
orderOutput = TRUE
)
df |
a data.frame with annotations corresponding to each row. Types of annotations are organized by columns.
For a given type of annotations, annotations are separated by |
sep_split |
Character string separating different annotation groups. |
sep |
Character string separating different annotations. |
idx_subset |
indexes of the foreground set. |
annotation_selected |
set of annotations on which to perform the analysis. Annotations selectd must be a subset of df's names. |
col_names |
df's column name containing gene names. |
two_sided |
logical, perform a two-sided hypergeometric test |
updateProgress |
logical, function to show progress in shiny app |
showProgress |
logical, show progress in console |
orderOutput |
logical, order annotations by enrichment p-values in the output data.frame |
a data.frame
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