Files in YAPSA

Yet Another Package for Signature Analysis

README.md R/plot_functions.R R/indels.R R/compare_SMCs.R R/LCD.R R/io_functions.R R/complex_functions.R R/confidence.R R/interact_foreign.R R/data.R R/indel_functions.R R/pkgname.R R/global.R R/SMC.R R/basic_functions.R vignettes/YAPSA.Rmd vignettes/vignette_confidenceIntervals.Rmd vignettes/vignette_exomes.Rmd vignettes/vignette_stratifiedAnalysis.Rmd vignettes/vignette_signature_specific_cutoffs.Rmd vignettes/vignettes_Indel.Rmd man/hclust_exposures.Rd man/GenomeOfNl_raw.Rd man/stat_plot_subgroups.Rd man/MutCat_indel_df.Rd man/create_indel_mut_cat_from_df.Rd man/LCD_SMC.Rd man/extract_names_from_gene_list.Rd man/stat_test_SMC.Rd man/shapiro_if_possible.Rd man/annotation_exposures_barplot.Rd man/run_kmer_frequency_normalization.Rd man/confidence_indel_only_calulation.Rd man/lymphomaNature2013_mutCat_df.Rd man/deriveSigInd_df.Rd man/aggregate_exposures_by_category.Rd man/confidence_indel_calulation.Rd man/normalizeMotifs_otherRownames.Rd man/make_catalogue_strata_df.Rd man/computeLogLik.Rd man/run_comparison_catalogues.Rd man/LCD_complex_cutoff.Rd man/run_kmer_frequency_correction.Rd man/transform_rownames_R_to_MATLAB.Rd man/attribute_sequence_contex_indel.Rd man/trellis_rainfall_plot.Rd man/SMC_perPID.Rd man/get_extreme_PIDs.Rd man/build_gene_list_for_pathway.Rd man/add_annotation.Rd man/SMC.Rd man/stat_test_subgroups.Rd man/run_comparison_general.Rd man/split_exposures_by_subgroups.Rd man/make_comparison_matrix.Rd man/create_indel_mutation_catalogue_from_df.Rd man/variateExpSingle.Rd man/plot_SMC.Rd man/cosineMatchDist.Rd man/exampleINDEL_YAPSA.Rd man/annotation_heatmap_exposures.Rd man/exampleYAPSA.Rd man/testSigs.Rd man/read_entry.Rd man/find_affected_PIDs.Rd man/merge_exposures.Rd man/variateExp.Rd man/make_strata_df.Rd man/melt_exposures.Rd man/cut_breaks_as_intervals.Rd man/plotExchangeSpectra_indel.Rd man/run_SMC.Rd man/add_as_fist_to_list.Rd man/plot_strata.Rd man/enrichSigs.Rd man/annotation_exposures_list_barplot.Rd man/sigs.Rd man/disambiguateVector.Rd man/plotExposuresConfidence_indel.Rd man/make_subgroups_df.Rd man/confIntExp.Rd man/plot_exposures.Rd man/cutoffs_pcawg.Rd man/sum_over_list_of_df.Rd man/targetCapture_cor_factors.Rd man/YAPSA.Rd man/translate_to_hg19.Rd man/getSequenceContext.Rd man/normalize_df_per_dim.Rd man/logLikelihood.Rd man/compare_expousre_sets.Rd man/compare_to_catalogues.Rd man/create_mutation_catalogue_from_VR.Rd man/temp_trellis_rainfall_plot.Rd man/repeat_df.Rd man/annotate_intermut_dist_PID.Rd man/test_gene_list_in_exposures.Rd man/annotate_intermut_dist_cohort.Rd man/compare_sets.Rd man/create_mutation_catalogue_from_df.Rd man/run_annotate_vcf_pl.Rd man/relateSigs.Rd man/correct_rounded.Rd man/attribution_of_indels.Rd man/complex_heatmap_exposures.Rd man/LCD.Rd man/cosineDist.Rd man/attribute_nucleotide_exchanges.Rd man/sigs_pcawg.Rd man/plotExposuresConfidence.Rd man/test_exposureAffected.Rd man/compare_SMCs.Rd man/stderrmean.Rd man/round_precision.Rd man/run_plot_strata_general.Rd man/exchange_colour_vector.Rd man/compare_exposures.Rd man/compute_comparison_stat_df.Rd man/trellis_rainfall_plot_old.Rd man/classify_indels.Rd man/cutoffs.Rd man/exome_mutCatRaw_df.Rd man/plotExchangeSpectra.Rd man/makeVRangesFromDataFrame.Rd man/exposures_barplot.Rd tests/testthat.R tests/testthat/test_complex_functions.R tests/testthat/test_basic_functions.R tests/testthat/test_LCD.R inst/doc/vignette_signature_specific_cutoffs.R inst/doc/vignette_confidenceIntervals.R inst/doc/YAPSA.Rmd inst/doc/vignette_exomes.R inst/doc/vignette_confidenceIntervals.Rmd inst/doc/vignette_exomes.Rmd inst/doc/YAPSA.R inst/doc/vignettes_Indel.R inst/doc/vignette_stratifiedAnalysis.R inst/doc/vignette_stratifiedAnalysis.Rmd inst/doc/vignette_signature_specific_cutoffs.Rmd inst/doc/vignettes_Indel.Rmd