Yet Another Package for Signature Analysis


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Documentation for package ‘YAPSA’ version 1.6.0

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YAPSA-package Generate R documentation from inline comments.
add_annotation Add information to an annotation data structure
add_as_fist_to_list Add an element as first entry to a list
aggregate_exposures_by_category Aggregate exposures by category
AlexCosmicArtif_sigInd_df Data for mutational signatures
AlexCosmicArtif_sig_df Data for mutational signatures
AlexCosmicValid_sigInd_df Data for mutational signatures
AlexCosmicValid_sig_df Data for mutational signatures
AlexInitialArtif_sigInd_df Data for mutational signatures
AlexInitialArtif_sig_df Data for mutational signatures
AlexInitialValid_sigInd_df Data for mutational signatures
AlexInitialValid_sig_df Data for mutational signatures
annotate_intermut_dist_cohort Annotate the intermutation distance of variants cohort-wide
annotate_intermut_dist_PID Annotate the intermutation distance of variants per PID
annotation_exposures_barplot Plot the exposures of a cohort with different layers of annotation
annotation_heatmap_exposures Heatmap to cluster the PIDs on their signature exposures (ComplexHeatmap)
attribute_nucleotide_exchanges Attribute the nucleotide exchange for an SNV
average_over_present Useful functions on data frames
build_gene_list_for_pathway Build a gene list for a given pathway name
chosen_AlexInitialArtif_sigInd_df Test and example data
chosen_signatures_indices_df Test and example data
compare_exposures Compares alternative exposures
compare_sets Compare two sets of signatures by cosine distance
compare_SMCs Compare all strata from different stratifications
compare_to_catalogues Compare one mutational catalogue to reference mutational catalogues
complex_heatmap_exposures Heatmap to cluster the PIDs on their signature exposures (ComplexHeatmap)
compute_comparison_stat_df Extract statistical measures for entity comparison
cosineDist Compute the cosine distance of two vectors
COSMIC_subgroups_df Test and example data
create_mutation_catalogue_from_df Create a Mutational Catalogue from a data frame
create_mutation_catalogue_from_VR Create a Mutational Catalogue from a VRanges Object
cutoffCosmicArtif_abs_df Cutoffs for a supervised analysis of mutational signatures.
cutoffCosmicArtif_rel_df Cutoffs for a supervised analysis of mutational signatures.
cutoffCosmicValid_abs_df Cutoffs for a supervised analysis of mutational signatures.
cutoffCosmicValid_rel_df Cutoffs for a supervised analysis of mutational signatures.
cutoffInitialArtif_abs_df Cutoffs for a supervised analysis of mutational signatures.
cutoffInitialArtif_rel_df Cutoffs for a supervised analysis of mutational signatures.
cutoffInitialValid_abs_df Cutoffs for a supervised analysis of mutational signatures.
cutoffInitialValid_rel_df Cutoffs for a supervised analysis of mutational signatures.
cutoffs Cutoffs for a supervised analysis of mutational signatures.
cut_breaks_as_intervals Wrapper for cut
exampleYAPSA Test and example data
exchange_colour_vector Colours codes for displaying SNVs
exposures_barplot Wrapper for enhanced_barplot
extract_names_from_gene_list Return gene names from gene lists
find_affected_PIDs Find samples affected
get_extreme_PIDs Return those PIDs which have an extreme pattern for signature exposure
hclust_exposures Cluster the PIDs according to their signature exposures
LCD Linear Combination Decomposition
LCD_complex_cutoff LCD with a signature-specific cutoff on exposures
LCD_complex_cutoff_perPID LCD with a signature-specific cutoff on exposures
lymphoma_Nature2013_COSMIC_cutoff_exposures_df Test and example data
lymphoma_Nature2013_raw_df Test and example data
lymphoma_PID_df Test and example data
lymphoma_test_df Test and example data
makeVRangesFromDataFrame Construct a VRanges Object from a data frame
make_catalogue_strata_df Group strata from different stratification axes
make_comparison_matrix Compute a similarity matrix for different strata
make_strata_df Group strata from different stratification axes
make_subgroups_df Make a custom data structure for subgroups
melt_exposures Generically melts exposure data frames
merge_exposures Merge exposure data frames
normalizeMotifs_otherRownames Normalize Somatic Motifs with different rownames
normalize_df_per_dim Useful functions on data frames
plotExchangeSpectra Plot the spectra of nucleotide exchanges
plot_exposures Plot the exposures of a cohort
plot_relative_exposures Plot the exposures of a cohort
plot_SMC Plot results of the Stratification of a Mutational Catalogue
plot_strata Plot all strata from different stratification axes together
rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df Test and example data
repeat_df Create a data frame with default values
run_annotate_vcf_pl Wrapper function to annotate addition information
run_comparison_catalogues Compare all strata from different stratifications
run_comparison_general Compare all strata from different stratifications
run_kmer_frequency_correction Provide comprehensive correction factors for kmer content
run_kmer_frequency_normalization Provide normalized correction factors for kmer content
run_plot_strata_general Wrapper function for 'plot_strata'
run_SMC Wrapper function for the Stratification of a Mutational Catalogue
sd_over_present Useful functions on data frames
shapiro_if_possible Wrapper for Shapiro test but allow for all identical values
sigs Data for mutational signatures
split_exposures_by_subgroups Split an exposures data frame by subgroups
stat_plot_subgroups Plot averaged signature exposures per subgroup
stat_test_SMC Apply statistical tests to a stratification (SMC)
stat_test_subgroups Test for differences in average signature exposures between subgroups
stderrmean Compute the standard error of the mean
stderrmean_over_present Useful functions on data frames
sum_over_list_of_df Elementwise sum over a list of (numerical) data frames
targetCapture_cor_factors Correction factors for different target capture kits
test_exposureAffected Test significance of association
test_gene_list_in_exposures Test if mutated PIDs are enriched in signatures
transform_rownames_deconstructSigs_to_YAPSA Change rownames from one naming convention to another
transform_rownames_MATLAB_to_R Change rownames from one naming convention to another
transform_rownames_nature_to_R Change rownames from one naming convention to another
transform_rownames_R_to_MATLAB Change rownames from one naming convention to another
transform_rownames_YAPSA_to_deconstructSigs Change rownames from one naming convention to another
translate_to_1kG Translate chromosome names to the hg19 naming convention
translate_to_hg19 Translate chromosome names to the hg19 naming convention
trellis_rainfall_plot Create a rainfall plot in a trellis structure
YAPSA Generate R documentation from inline comments.