YAPSA
Yet Another Package for Signature Analysis

Package index
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Functions
277
Source code
24
Man pages
104
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YAPSA: Yet Another Package for Signature Analysis
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API for YAPSA
Yet Another Package for Signature Analysis

Global functions
AlexCosmicArtif_sigInd_df Man page
AlexCosmicArtif_sig_df Man page
AlexCosmicValid_sigInd_df Man page
AlexCosmicValid_sig_df Man page
AlexInitialArtif_sigInd_df Man page
AlexInitialArtif_sig_df Man page
AlexInitialValid_sigInd_df Man page
AlexInitialValid_sig_df Man page
COSMIC_subgroups_df Man page
GenomeOfNl_raw Man page
LCD Man page Source code
LCD_SMC Man page Source code
LCD_complex_cutoff Man page Source code
LCD_complex_cutoff_combined Man page Source code
LCD_complex_cutoff_consensus Man page Source code
LCD_complex_cutoff_perPID Man page Source code
LCD_cutoff Source code
MutCat_indel_df Man page
PCAWG_SP_ID_sigInd_df Man page
PCAWG_SP_ID_sigs_df Man page
PCAWG_SP_SBS_sigInd_Artif_df Man page
PCAWG_SP_SBS_sigInd_Real_df Man page
PCAWG_SP_SBS_sigs_Artif_df Man page
PCAWG_SP_SBS_sigs_Real_df Man page
SMC Man page Source code
SMC_perPID Man page
YAPSA Man page
add_annotation Man page Source code
add_as_fist_to_list Man page Source code
add_rainfalls_track Source code
add_rectangles_track Source code
adjust_number_of_columns_in_list_of_catalogues Source code
aggregate_exposures_by_category Man page Source code
annotate_intermut_dist_PID Man page Source code
annotate_intermut_dist_cohort Man page Source code
annotation_exposures_barplot Man page Source code
annotation_exposures_list_barplot Man page Source code
annotation_heatmap_exposures Man page Source code
attribute_nucleotide_exchanges Man page Source code
attribute_sequence_contex_indel Man page Source code
attribution_of_indels Man page Source code
average_over_present Man page Source code
build_gene_list_for_pathway Man page Source code
check_bedtools Source code
check_perl Source code
chosen_AlexInitialArtif_sigInd_df Man page
chosen_signatures_indices_df Man page
classify_indels Man page Source code
compare_SMCs Man page Source code
compare_exposures Man page Source code
compare_expousre_sets Man page Source code
compare_sets Man page Source code
compare_to_catalogues Man page Source code
complex_heatmap_exposures Man page Source code
computeLogLik Man page Source code
compute_comparison_stat_df Man page Source code
confIntExp Man page Source code
confidence_indel_calulation Man page Source code
confidence_indel_only_calulation Man page Source code
correct_rounded Man page Source code
cosineDist Man page Source code
cosineMatchDist Man page Source code
create_indel_mut_cat_from_df Man page Source code
create_indel_mutation_catalogue_from_df Man page Source code
create_mutation_catalogue_from_VR Man page Source code
create_mutation_catalogue_from_df Man page Source code
cut_breaks_as_intervals Man page Source code
cutoffCosmicArtif_abs_df Man page
cutoffCosmicArtif_rel_df Man page
cutoffCosmicValid_abs_df Man page
cutoffCosmicValid_rel_df Man page
cutoffInitialArtif_abs_df Man page
cutoffInitialArtif_rel_df Man page
cutoffInitialValid_abs_df Man page
cutoffInitialValid_rel_df Man page
cutoffPCAWG_ID_WGS_Pid_df Man page
cutoffPCAWG_SBS_WGSWES_artifPid_df Man page
cutoffPCAWG_SBS_WGSWES_realPid_df Man page
cutoffs Man page
cutoffs_pcawg Man page
deriveSigInd_df Man page Source code
disambiguateVector Man page Source code
enhanced_barplot Source code
enrichSigs Man page Source code
exampleINDEL_YAPSA Man page
exampleYAPSA Man page
exchange_colour_vector Man page
exome_mutCatRaw_df Man page
exposures_barplot Man page Source code
extract_names_from_gene_list Man page Source code
find_affected_PIDs Man page Source code
getSequenceContext Man page Source code
get_extreme_PIDs Man page Source code
hclust_exposures Man page Source code
logLikelihood Man page Source code
lymphomaNature2013_mutCat_df Man page
lymphoma_Nature2013_COSMIC_cutoff_exposures_df Man page
lymphoma_Nature2013_raw_df Man page
lymphoma_PID_df Man page
lymphoma_test_df Man page
makeVRangesFromDataFrame Man page Source code
make_catalogue_strata_df Man page Source code
make_comparison_matrix Man page Source code
make_strata_df Man page Source code
make_subgroups_df Man page Source code
melt_exposures Man page Source code
merge_exposures Man page Source code
norm_res Source code
normalizeMotifs_otherRownames Man page Source code
normalize_df_per_dim Man page Source code
plotExchangeSpectra Man page Source code
plotExchangeSpectra_indel Man page
plotExposuresConfidence Man page Source code
plotExposuresConfidence_indel Man page Source code
plot_SMC Man page Source code
plot_SMC_PID_facet Source code
plot_SMC_old Source code
plot_colour_legend_subgroups Source code
plot_exposures Man page Source code
plot_exposures_old Source code
plot_group_facet Source code
plot_relative_exposures Man page Source code
plot_strata Man page Source code
preprocess_VRanges Source code
preprocess_data.frame Source code
read_entry Man page Source code
read_list Man page Source code
rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df Man page
relateSigs Man page Source code
repeat_df Man page Source code
res Source code
round_precision Man page Source code
run_SMC Man page Source code
run_annotate_vcf_pl Man page Source code
run_bedtools_getfasta Source code
run_comparison_catalogues Man page Source code
run_comparison_general Man page Source code
run_kmer_frequency_correction Man page Source code
run_kmer_frequency_normalization Man page Source code
run_kmer_frequency_pl Source code
run_plot_strata_general Man page Source code
save_mutation_catalogue Source code
save_stratified_vcf_like_df Source code
sd_over_present Man page Source code
shapiro_if_possible Man page Source code
sigs Man page
sigs_pcawg Man page
split_exposures_by_subgroups Man page Source code
stat_plot_subgroups Man page Source code
stat_plot_subgroups_old Source code
stat_test_SMC Man page Source code
stat_test_subgroups Man page Source code
stderrmean Man page Source code
stderrmean_over_present Man page Source code
stratify_and_create_mutational_catalogue Source code
stratify_vcf_like_df Source code
sum_over_list_of_df Man page Source code
targetCapture_cor_factors Man page
temp_trellis_rainfall_plot Man page Source code
testSigs Man page Source code
test_exposureAffected Man page Source code
test_gene_list_in_exposures Man page Source code
transform_rownames_MATLAB_to_R Man page Source code
transform_rownames_R_to_MATLAB Man page Source code
transform_rownames_YAPSA_to_deconstructSigs Man page Source code
transform_rownames_deconstructSigs_to_YAPSA Man page Source code
transform_rownames_nature_to_R Man page Source code
translate_to_1kG Man page Source code
translate_to_hg19 Man page Source code
trellis_rainfall_plot Man page Source code
trellis_rainfall_plot_old Man page Source code
uniquify Source code
variateExp Man page Source code
variateExpSingle Man page Source code
vplayout Source code
YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.

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