Benchmarking

DESCRIPTION

@@ -14,7 +14,7 @@ biocViews:
     SomaticMutation,
     VariantAnnotation
 Depends:
-    R (>= 4.0.0), 
+    R (>= 4.0.0),
     NMF
 Imports:
     SummarizedExperiment,
@@ -48,7 +48,6 @@ Imports:
     BSgenome.Hsapiens.UCSC.hg38,
     BSgenome.Mmusculus.UCSC.mm9,
     BSgenome.Mmusculus.UCSC.mm10,
-    deconstructSigs,
     decompTumor2Sig,
     topicmodels,
     ggrepel,
@@ -63,7 +62,9 @@ Imports:
     stringi,
     tidyverse,
     ggpubr,
-    Matrix (>= 1.6.1)
+    Matrix (>= 1.6.4),
+    scales,
+    lsei
 Suggests:
     TCGAbiolinks,
     shinyBS,

NAMESPACE

@@ -1,18 +1,42 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
+export("adjustment_threshold<-")
+export("description<-")
 export("exposures<-")
+export("final_comparison<-")
+export("final_pred<-")
+export("ground_truth<-")
+export("indv_benchmarks<-")
+export("initial_comparison<-")
+export("initial_pred<-")
+export("intermediate_comparison<-")
+export("intermediate_pred<-")
+export("method_id<-")
+export("method_view_summary<-")
 export("samp_annot<-")
+export("sig_view_summary<-")
 export("signatures<-")
 export("tables<-")
+export("threshold<-")
 export("umap<-")
 export("variants<-")
 export(add_flank_to_variants)
+export(adjustment_threshold)
 export(annotate_replication_strand)
 export(annotate_transcript_strand)
 export(annotate_variant_length)
 export(annotate_variant_type)
 export(auto_predict_grid)
+export(benchmark)
+export(benchmark_compare_results)
+export(benchmark_get_entry)
+export(benchmark_get_prediction)
+export(benchmark_plot_comparison)
+export(benchmark_plot_composite_exposures)
+export(benchmark_plot_duplicate_exposures)
+export(benchmark_plot_exposures)
+export(benchmark_plot_signatures)
 export(build_custom_table)
 export(build_standard_table)
 export(built_tables)
@@ -23,8 +47,12 @@ export(compare_cosmic_v2)
 export(compare_cosmic_v3)
 export(compare_results)
 export(cosmic_v2_subtype_map)
-export(create_musica)
+export(create_benchmark)
+export(create_musica_from_counts)
+export(create_musica_from_variants)
+export(create_musica_result)
 export(create_umap)
+export(description)
 export(discover_signatures)
 export(drop_annotation)
 export(exposure_differential_analysis)
@@ -36,37 +64,53 @@ export(extract_variants_from_maf_file)
 export(extract_variants_from_matrix)
 export(extract_variants_from_vcf)
 export(extract_variants_from_vcf_file)
+export(final_comparison)
+export(final_pred)
 export(generate_result_grid)
 export(get_musica)
+export(ground_truth)
+export(indv_benchmarks)
+export(initial_comparison)
+export(initial_pred)
+export(intermediate_comparison)
+export(intermediate_pred)
 export(k_select)
+export(method_id)
+export(method_view_summary)
 export(musicatk)
 export(name_signatures)
 export(plot_cluster)
+export(plot_comparison)
 export(plot_differential_analysis)
 export(plot_exposures)
 export(plot_heatmap)
 export(plot_sample_counts)
 export(plot_sample_reconstruction_error)
 export(plot_signatures)
 export(plot_umap)
+export(predict_and_benchmark)
 export(predict_exposure)
 export(rc)
 export(samp_annot)
 export(sample_names)
 export(select_genome)
+export(sig_view_summary)
 export(signatures)
 export(subset_musica_by_annotation)
 export(subset_musica_by_counts)
 export(subset_variant_by_type)
 export(subset_variants_by_samples)
 export(table_selected)
 export(tables)
+export(threshold)
 export(umap)
 export(variants)
 exportClasses(count_table)
+exportClasses(full_benchmark)
 exportClasses(musica)
 exportClasses(musica_result)
 exportClasses(musica_result_grid)
+exportClasses(single_benchmark)
 import(dplyr)
 import(ggplot2)
 import(tidyr)