Imports a YAML file and validates it against the block registry.
Examples
example_file <- system.file("extdata", "bcl11a_rs1427407_example.csv",
package = "AlphaVaR")
obj <- av_import_csv(example_file)
#> Reading bcl11a_rs1427407_example.csv ...
yaml_file <- file.path(tempdir(), "shared_template.yaml")
av_report_save_template(av_report_template_default(), yaml_file)
spec <- av_report_load_template(yaml_file)
spec
#> === AlphaVarReportSpec ===
#> Title: AlphaGenome Variant Analysis Report
#> Blocks: 27
#>
#> [1] [section] Section Header
#> [2] [text] Markdown Text Block
#> [3] [table] QC Summary Table
#> [4] [plot] Ridge Plot
#> [5] [section] Section Header
#> [6] [text] Markdown Text Block
#> [7] [plot] Genome Browser View (Interval)
#> [8] [section] Section Header
#> [9] [text] Markdown Text Block
#> [10] [plot] Cumulative Distribution (ECDF)
#> [11] [plot] Effect Directionality
#> [12] [table] Enrichment Statistics Table
#> [13] [plot] Enrichment Volcano Plot
#> [14] [table] Gene Impact Table
#> [15] [section] Section Header
#> [16] [text] Markdown Text Block
#> [17] [plot] Enrichment Volcano Plot
#> [18] [table] Enrichment Statistics Table
#> [19] [plot] Specificity (Tau) per Unit
#> [20] [table] Gene Impact Table
#> [21] [section] Section Header
#> [22] [table] Target Gene Assignment Table
#> [23] [table] Gene Impact Table
#> [24] [plot] Ranking Boxplot
#> [25] [plot] Ridge Plot
#> [26] [section] Section Header
#> [27] [table] Variant Table
# A template travels between datasets, so its grouping columns are only
# guaranteed to exist in the dataset it was written for.
group_cols <- unique(unlist(lapply(spec$blocks, function(b) b$params$group_by)))
group_cols %in% names(obj$data)
#> [1] TRUE TRUE TRUE