Index

Symbols

1_extractPCS module 2_computeWindows module 3_setupEvolTimes module 4_estimateEvolTimes module 5_sampleEvolTimes module

6_1_plotFig_PcsDistribComp module 6_2_plotFig_EvolTimesComp module 6_3_plotFig_MutRatesComp module 6_4_plotFig_FuncClasses module

A

author (6_3_plotFig_MutRatesComp.MutRateStudy attribute)

C

checkInputFiles() (in module 2_computeWindows) checkPCS() (1_extractPCS.PcsSingleCheck method) checkPCSrevQ() (in module 1_extractPCS) checkPCSrevT() (in module 1_extractPCS) checkPCSsize() (in module 1_extractPCS) checkPCSsizeDistribFiles() (in module 3_setupEvolTimes) checkSpecies() (in module 1_extractPCS)

computeDistribQuantile() (in module 6_3_plotFig_MutRatesComp) computeEvolTimeEmpty() (in module 6_3_plotFig_MutRatesComp) computePCScoords() (in module 1_extractPCS) computePos() (in module 1_extractPCS) computeSetupInfo_winRefSize() (in module 3_setupEvolTimes) computeWindows() (in module 2_computeWindows) consistencyCheck() (in module 2_computeWindows) createLines() (in module 6_3_plotFig_MutRatesComp)

D

distribPCS_all() (in module 2_computeWindows)

distribPCS_single() (in module 2_computeWindows)

E

estimateEvolTimes_winRefSize() (in module 4_estimateEvolTimes)

F

findBin() (in module 6_1_plotFig_PcsDistribComp)

G

get_aspect() (in module 6_4_plotFig_FuncClasses) getAnnotOrder() (in module 6_4_plotFig_FuncClasses) getAnnotTitles() (in module 6_4_plotFig_FuncClasses) getColors() (in module 6_4_plotFig_FuncClasses) getDirectEstimates() (in module 6_3_plotFig_MutRatesComp) getDistances() (in module 6_2_plotFig_EvolTimesComp) getEmptyWindows() (in module 6_2_plotFig_EvolTimesComp) (in module 6_3_plotFig_MutRatesComp)

getExtrapolatedEstimates() (in module 6_3_plotFig_MutRatesComp) getIndirectEstimates() (in module 6_3_plotFig_MutRatesComp) getNewEstimates() (in module 6_3_plotFig_MutRatesComp) getReferenceValues() (in module 3_setupEvolTimes) getSampleSizeRef() (in module 4_estimateEvolTimes) groupWindowsByAnnotType() (in module 6_4_plotFig_FuncClasses)

I

initializeOutputs() (in module 5_sampleEvolTimes) initializePCSchecks() (in module 1_extractPCS) initParallelInputs() (in module 3_setupEvolTimes) (in module 4_estimateEvolTimes) (in module 5_sampleEvolTimes)

isCompatible() (in module 1_extractPCS) isContiguous() (in module 2_computeWindows) isOverlap() (in module 2_computeWindows)

L

loadAnnotations() (in module 6_4_plotFig_FuncClasses) loadData() (in module 6_2_plotFig_EvolTimesComp) loadEvolEstimates() (in module 6_4_plotFig_FuncClasses)

loadObservedValues() (in module 3_setupEvolTimes) loadOurData() (in module 6_2_plotFig_EvolTimesComp) (in module 6_3_plotFig_MutRatesComp)

M

makeAnnotationMatrix() (in module 6_4_plotFig_FuncClasses) makeColormap() (in module 6_2_plotFig_EvolTimesComp) makeFigure2() (in module 6_1_plotFig_PcsDistribComp) makeFigure3() (in module 6_2_plotFig_EvolTimesComp) makeFigure4() (in module 6_3_plotFig_MutRatesComp) makeFigure5() (in module 6_4_plotFig_FuncClasses) makeFigureSuppS8() (in module 6_4_plotFig_FuncClasses) meanEvolTimes() (in module 6_2_plotFig_EvolTimesComp) (in module 6_3_plotFig_MutRatesComp) mergePCS_all() (in module 2_computeWindows) mergePCS_pairwise() (in module 2_computeWindows) mergePCS_pairwise_check() (in module 2_computeWindows) mergePCS_pairwise_findPos() (in module 2_computeWindows) mergePCS_pairwise_updLst() (in module 2_computeWindows)

methodType (6_3_plotFig_MutRatesComp.MutRateStudy attribute) module 1_extractPCS 2_computeWindows 3_setupEvolTimes 4_estimateEvolTimes 5_sampleEvolTimes 6_1_plotFig_PcsDistribComp 6_2_plotFig_EvolTimesComp 6_3_plotFig_MutRatesComp 6_4_plotFig_FuncClasses mutRatePPPY (6_3_plotFig_MutRatesComp.MutRateStudy attribute) mutRatePPPY_lb (6_3_plotFig_MutRatesComp.MutRateStudy attribute) mutRatePPPY_ub (6_3_plotFig_MutRatesComp.MutRateStudy attribute) MutRateStudy (class in 6_3_plotFig_MutRatesComp)

P

parseMapping() (in module 6_2_plotFig_EvolTimesComp) PcsSingleCheck (class in 1_extractPCS) performPCSchecks() (in module 1_extractPCS) plotComparisonEvolTimes() (in module 6_2_plotFig_EvolTimesComp) plotErrorRect() (in module 6_3_plotFig_MutRatesComp) plotFuncClassDistrib() (in module 6_4_plotFig_FuncClasses) plotIcon() (in module 6_3_plotFig_MutRatesComp) plotMutationRateComparison() (in module 6_3_plotFig_MutRatesComp) plotMutationRatePerType() (in module 6_3_plotFig_MutRatesComp)

plotPCSsizeDistribBig() (in module 6_1_plotFig_PcsDistribComp) plotTauDistribSampled_sum() (in module 6_1_plotFig_PcsDistribComp) prepareDataForPlotting() (in module 6_1_plotFig_PcsDistribComp) print() (1_extractPCS.PcsSingleCheck method) printIgnoredWindows() (in module 4_estimateEvolTimes) printPCS() (in module 2_computeWindows) processIteration() (in module 3_setupEvolTimes) (in module 4_estimateEvolTimes) (in module 5_sampleEvolTimes) publYear (6_3_plotFig_MutRatesComp.MutRateStudy attribute)

R

readChains() (in module 1_extractPCS) readDNA() (in module 1_extractPCS) readSampleSizeRefs() (in module 4_estimateEvolTimes)

readSetup() (in module 4_estimateEvolTimes) reset() (1_extractPCS.PcsSingleCheck method) reverseComplement() (in module 1_extractPCS) rgba_to_hex() (in module 6_2_plotFig_EvolTimesComp)

S

sample_pcs() (in module 5_sampleEvolTimes) sampleEvolTimes() (in module 5_sampleEvolTimes)

selectEvolTimes() (in module 3_setupEvolTimes) sortAnnotations() (in module 6_4_plotFig_FuncClasses)

U

ucscName (6_3_plotFig_MutRatesComp.MutRateStudy attribute)

Y

yLabels() (in module 6_3_plotFig_MutRatesComp)