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.

AuthorDaniel Huebschmann, Zuguang Gu, Matthias Schlesner
Date of publicationNone
MaintainerDaniel Huebschmann <huebschmann.daniel@googlemail.com>
LicenseGPL-3
Version1.0.0

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.

Functions

add_annotation Man page
add_as_fist_to_list Man page
aggregate_exposures_by_category Man page
AlexCosmicArtif_sig_df Man page
AlexCosmicArtif_sigInd_df Man page
AlexCosmicValid_sig_df Man page
AlexCosmicValid_sigInd_df Man page
AlexInitialArtif_sig_df Man page
AlexInitialArtif_sigInd_df Man page
AlexInitialValid_sig_df Man page
AlexInitialValid_sigInd_df Man page
annotate_intermut_dist_cohort Man page
annotate_intermut_dist_PID Man page
annotation_exposures_barplot Man page
annotation_heatmap_exposures Man page
attribute_nucleotide_exchanges Man page
average_over_present Man page
build_gene_list_for_pathway Man page
chosen_AlexInitialArtif_sigInd_df Man page
chosen_signatures_indices_df Man page
compare_exposures Man page
compare_sets Man page
compare_SMCs Man page
compare_to_catalogues Man page
complex_heatmap_exposures Man page
compute_comparison_stat_df Man page
cosineDist Man page
COSMIC_subgroups_df Man page
create_mutation_catalogue_from_df Man page
create_mutation_catalogue_from_VR Man page
cut_breaks_as_intervals Man page
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
exampleYAPSA Man page
exchange_colour_vector Man page
exposures_barplot Man page
extract_names_from_gene_list Man page
find_affected_PIDs Man page
get_extreme_PIDs Man page
hclust_exposures Man page
LCD Man page
LCD_complex_cutoff Man page
LCD_complex_cutoff_perPID 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
make_catalogue_strata_df Man page
make_comparison_matrix Man page
make_strata_df Man page
make_subgroups_df Man page
makeVRangesFromDataFrame Man page
melt_exposures Man page
merge_exposures Man page
normalize_df_per_dim Man page
normalizeMotifs_otherRownames Man page
plotExchangeSpectra Man page
plot_exposures Man page
plot_relative_exposures Man page
plot_SMC Man page
plot_strata Man page
rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df Man page
repeat_df Man page
run_annotate_vcf_pl Man page
run_comparison_catalogues Man page
run_comparison_general Man page
run_kmer_frequency_correction Man page
run_kmer_frequency_normalization Man page
run_plot_strata_general Man page
run_SMC Man page
sd_over_present Man page
shapiro_if_possible Man page
sigs Man page
split_exposures_by_subgroups Man page
stat_plot_subgroups Man page
stat_test_SMC Man page
stat_test_subgroups Man page
stderrmean Man page
stderrmean_over_present Man page
sum_over_list_of_df Man page
targetCapture_cor_factors Man page
test_exposureAffected Man page
test_gene_list_in_exposures Man page
transform_rownames_deconstructSigs_to_YAPSA Man page
transform_rownames_MATLAB_to_R Man page
transform_rownames_nature_to_R Man page
transform_rownames_R_to_MATLAB Man page
transform_rownames_YAPSA_to_deconstructSigs Man page
translate_to_1kG Man page
translate_to_hg19 Man page
trellis_rainfall_plot Man page
YAPSA Man page
YAPSA-package Man page

Files

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

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