YAPSA: Yet Another Package for Signature Analysis

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.

Author
Daniel Huebschmann, Zuguang Gu, Matthias Schlesner
Date of publication
None
Maintainer
Daniel Huebschmann <huebschmann.daniel@googlemail.com>
License
GPL-3
Version
1.0.0

View on Bioconductor

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.

Files in this package

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