YAPSA: Yet Another Package for Signature Analysis
Version 1.2.0

This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.

Browse man pages Browse package API and functions Browse package files

AuthorDaniel Huebschmann, Zuguang Gu, Matthias Schlesner
Bioconductor views BiologicalQuestion Clustering DNASeq GenomicVariation Sequencing SomaticMutation StatisticalMethod Visualization
Date of publicationNone
MaintainerDaniel Huebschmann <huebschmann.daniel@googlemail.com>
LicenseGPL-3
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("YAPSA")

Man pages

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
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_heatmap_exposures: Heatmap to cluster the PIDs on their signature exposures...
attribute_nucleotide_exchanges: Attribute the nucleotide exchange for an SNV
build_gene_list_for_pathway: Build a gene list for a given pathway name
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...
complex_heatmap_exposures: Heatmap to cluster the PIDs on their signature exposures...
compute_comparison_stat_df: Extract statistical measures for entity comparison
cosineDist: Compute the cosine distance of two vectors
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
cut_breaks_as_intervals: Wrapper for cut
cutoffs: Cutoffs for a supervised analysis of mutational signatures.
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...
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
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
makeVRangesFromDataFrame: Construct a VRanges Object from a data frame
melt_exposures: Generically melts exposure data frames
merge_exposures: Merge exposure data frames
normalize_df_per_dim: Useful functions on data frames
normalizeMotifs_otherRownames: Normalize Somatic Motifs with different rownames
plotExchangeSpectra: Plot the spectra of nucleotide exchanges
plot_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
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...
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...
stderrmean: Compute the standard error of the mean
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_R_to_MATLAB: Change rownames from one naming convention to another
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.

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
LCD Man page Source code
LCD_SMC Source code
LCD_complex_cutoff Man page Source code
LCD_complex_cutoff_perPID Man page Source code
LCD_cutoff Source code
SMC Source code
YAPSA Man page
YAPSA-package Man page
add_annotation Man page Source code
add_as_fist_to_list Man page 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_heatmap_exposures Man page Source code
attribute_nucleotide_exchanges 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
compare_SMCs Man page Source code
compare_exposures Man page Source code
compare_sets Man page Source code
compare_to_catalogues Man page Source code
complex_heatmap_exposures Man page Source code
compute_comparison_stat_df Man page Source code
cosineDist 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
cutoffs Man page
enhanced_barplot Source code
exampleYAPSA Man page
exchange_colour_vector Man page
exposures_barplot Man page Source code
extract_names_from_gene_list Man page Source code
find_affected_PIDs Man page Source code
get_extreme_PIDs Man page Source code
hclust_exposures Man page Source code
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
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
rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df Man page
repeat_df Man page Source code
res 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
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
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
vplayout Source code

Files

CONTRIBUTORS
DESCRIPTION
LICENSE.txt
NAMESPACE
NEWS
R
R/LCD.R
R/SMC.R
R/basic_functions.R
R/compare_SMCs.R
R/complex_functions.R
R/data.R
R/interact_foreign.R
R/pkgname.R
R/plot_functions.R
README.md
README_files
README_files/figure-html
README_files/figure-html/SMC_mut_density-1.png
README_files/figure-html/apply_heatmap_exposures-1.png
README_files/figure-html/cluster_PIDs_sig_info-1.png
README_files/figure-html/exposures_barplot_LCD-1.png
README_files/figure-html/exposures_barplot_LCD_sig_ind-1.png
README_files/figure-html/exposures_barplot_abs_cutoffGen-1.png
README_files/figure-html/exposures_barplot_abs_cutoffSpec-1.png
README_files/figure-html/exposures_barplot_abs_cutoffZero-1.png
README_files/figure-html/exposures_barplot_rel_cutoffGen-1.png
README_files/figure-html/exposures_barplot_rel_cutoffSpec-1.png
README_files/figure-html/exposures_barplot_rel_cutoffZero-1.png
README_files/figure-html/make_rainfall_plot-1.png
build
build/vignette.rds
data
data/cutoffs.rda
data/exchange_colour_vector.rda
data/lymphoma_Nature2013_raw.rda
data/lymphoma_PID.rda
data/lymphoma_cohort_LCD_results.rda
data/lymphoma_test.rda
data/sigs.rda
data/targetCapture_cor_factors.rda
inst
inst/doc
inst/doc/YAPSA.R
inst/doc/YAPSA.Rmd
inst/doc/YAPSA.html
inst/foreign
inst/foreign/annotate_vcf.pl
inst/foreign/kmer_frequencies.pl
man
man/LCD.Rd
man/LCD_complex_cutoff.Rd
man/YAPSA.Rd
man/add_annotation.Rd
man/add_as_fist_to_list.Rd
man/aggregate_exposures_by_category.Rd
man/annotate_intermut_dist_PID.Rd
man/annotate_intermut_dist_cohort.Rd
man/annotation_exposures_barplot.Rd
man/annotation_heatmap_exposures.Rd
man/attribute_nucleotide_exchanges.Rd
man/build_gene_list_for_pathway.Rd
man/compare_SMCs.Rd
man/compare_exposures.Rd
man/compare_sets.Rd
man/compare_to_catalogues.Rd
man/complex_heatmap_exposures.Rd
man/compute_comparison_stat_df.Rd
man/cosineDist.Rd
man/create_mutation_catalogue_from_VR.Rd
man/create_mutation_catalogue_from_df.Rd
man/cut_breaks_as_intervals.Rd
man/cutoffs.Rd
man/exampleYAPSA.Rd
man/exchange_colour_vector.Rd
man/exposures_barplot.Rd
man/extract_names_from_gene_list.Rd
man/find_affected_PIDs.Rd
man/get_extreme_PIDs.Rd
man/hclust_exposures.Rd
man/makeVRangesFromDataFrame.Rd
man/make_catalogue_strata_df.Rd
man/make_comparison_matrix.Rd
man/make_strata_df.Rd
man/make_subgroups_df.Rd
man/melt_exposures.Rd
man/merge_exposures.Rd
man/normalizeMotifs_otherRownames.Rd
man/normalize_df_per_dim.Rd
man/plotExchangeSpectra.Rd
man/plot_SMC.Rd
man/plot_exposures.Rd
man/plot_strata.Rd
man/repeat_df.Rd
man/run_SMC.Rd
man/run_annotate_vcf_pl.Rd
man/run_comparison_catalogues.Rd
man/run_comparison_general.Rd
man/run_kmer_frequency_correction.Rd
man/run_kmer_frequency_normalization.Rd
man/run_plot_strata_general.Rd
man/shapiro_if_possible.Rd
man/sigs.Rd
man/split_exposures_by_subgroups.Rd
man/stat_plot_subgroups.Rd
man/stat_test_SMC.Rd
man/stat_test_subgroups.Rd
man/stderrmean.Rd
man/sum_over_list_of_df.Rd
man/targetCapture_cor_factors.Rd
man/test_exposureAffected.Rd
man/test_gene_list_in_exposures.Rd
man/transform_rownames_R_to_MATLAB.Rd
man/translate_to_hg19.Rd
man/trellis_rainfall_plot.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_LCD.R
tests/testthat/test_basic_functions.R
tests/testthat/test_complex_functions.R
vignettes
vignettes/NMF.png
vignettes/YAPSA.Rmd
YAPSA documentation built on May 20, 2017, 11:01 p.m.