Build path to the enrichment results — build_enrichment_path • shinyngs

Build path to the enrichment results

Usage

build_enrichment_path(template, contrast_info, geneset_type, direction = NULL)

Arguments

template: A string, such as "/path/to/folder/{contrast_name}-{geneset_type}.csv" or "./{contrast_name}/{geneset_type}/report_for_{target|reference}.csv"
contrast_info: A list with contrast details: `id`, `reference`, and `target`, to be replaced in template.
geneset_type: The name of the geneset type, to be replaced in the template
direction: Either `"up"`, `"down"` or `NULL`, used to determine how the replacement will happen.

Value

A string similar to template, but with the templates replaced

Details

The template accepts the following:

{contrast_name}: Will be replaced by contrast_info$id argument
{geneset_type}: Will be replaced by the geneset_type argument
{target|reference}: If the direction argument is "up", will be replaced with contrast_info$target, if it is "down", contrast_info$reference will be used instead.

Examples

build_enrichment_path(
  template = "./{contrast_name}/{geneset_type}/report_for_{target|reference}.csv",
  contrast_info = list(id = "disease_vs_ctrl", reference = "control", target = "disease"),
  geneset_type = "m2.cp.v2024.1.Mm.entrez",
  direction = "up"
)
#> [1] "./disease_vs_ctrl/m2.cp.v2024.1.Mm.entrez/report_for_disease.csv"