Man pages for huebschm/YAPSA
Yet Another Package for Signature Analysis

add_annotationAdd information to an annotation data structure
add_as_fist_to_listAdd an element as first entry to a list
aggregate_exposures_by_categoryAggregate exposures by category
annotate_intermut_dist_cohortAnnotate the intermutation distance of variants cohort-wide
annotate_intermut_dist_PIDAnnotate the intermutation distance of variants per PID
annotation_exposures_barplotPlot the exposures of a cohort with different layers of...
annotation_heatmap_exposuresHeatmap to cluster the PIDs on their signature exposures...
attribute_nucleotide_exchangesAttribute the nucleotide exchange for an SNV
build_gene_list_for_pathwayBuild a gene list for a given pathway name
compare_exposuresCompares alternative exposures
compare_setsCompare two sets of signatures by cosine distance
compare_SMCsCompare all strata from different stratifications
compare_to_cataloguesCompare one mutational catalogue to reference mutational...
complex_heatmap_exposuresHeatmap to cluster the PIDs on their signature exposures...
compute_comparison_stat_dfExtract statistical measures for entity comparison
cosineDistCompute the cosine distance of two vectors
create_mutation_catalogue_from_dfCreate a Mutational Catalogue from a data frame
create_mutation_catalogue_from_VRCreate a Mutational Catalogue from a VRanges Object
cut_breaks_as_intervalsWrapper for cut
cutoffsCutoffs for a supervised analysis of mutational signatures.
exampleYAPSATest and example data
exchange_colour_vectorColours codes for displaying SNVs
exposures_barplotWrapper for enhanced_barplot
extract_names_from_gene_listReturn gene names from gene lists
find_affected_PIDsFind samples affected
get_extreme_PIDsReturn those PIDs which have an extreme pattern for signature...
hclust_exposuresCluster the PIDs according to their signature exposures
LCDLinear Combination Decomposition
LCD_complex_cutoffLCD with a signature-specific cutoff on exposures
make_catalogue_strata_dfGroup strata from different stratification axes
make_comparison_matrixCompute a similarity matrix for different strata
make_strata_dfGroup strata from different stratification axes
make_subgroups_dfMake a custom data structure for subgroups
makeVRangesFromDataFrameConstruct a VRanges Object from a data frame
melt_exposuresGenerically melts exposure data frames
merge_exposuresMerge exposure data frames
normalize_df_per_dimUseful functions on data frames
normalizeMotifs_otherRownamesNormalize Somatic Motifs with different rownames
plotExchangeSpectraPlot the spectra of nucleotide exchanges
plot_exposuresPlot the exposures of a cohort
plot_SMCPlot results of the Stratification of a Mutational Catalogue
plot_strataPlot all strata from different stratification axes together
repeat_dfCreate a data frame with default values
run_annotate_vcf_plWrapper function to annotate addition information
run_comparison_cataloguesCompare all strata from different stratifications
run_comparison_generalCompare all strata from different stratifications
run_kmer_frequency_correctionProvide comprehensive correction factors for kmer content
run_kmer_frequency_normalizationProvide normalized correction factors for kmer content
run_plot_strata_generalWrapper function for 'plot_strata'
run_SMCWrapper function for the Stratification of a Mutational...
shapiro_if_possibleWrapper for Shapiro test but allow for all identical values
sigsData for mutational signatures
split_exposures_by_subgroupsSplit an exposures data frame by subgroups
stat_plot_subgroupsPlot averaged signature exposures per subgroup
stat_test_SMCApply statistical tests to a stratification (SMC)
stat_test_subgroupsTest for differences in average signature exposures between...
stderrmeanCompute the standard error of the mean
sum_over_list_of_dfElementwise sum over a list of (numerical) data frames
targetCapture_cor_factorsCorrection factors for different target capture kits
test_exposureAffectedTest significance of association
test_gene_list_in_exposuresTest if mutated PIDs are enriched in signatures
transform_rownames_R_to_MATLABChange rownames from one naming convention to another
translate_to_hg19Translate chromosome names to the hg19 naming convention
trellis_rainfall_plotCreate a rainfall plot in a trellis structure
YAPSAGenerate R documentation from inline comments.
huebschm/YAPSA documentation built on May 17, 2019, 9:11 p.m.