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Functions640 in github.com/BoevaLab/FREEC

⨍ Functions 640◇ Types & classes 40

↓ 4 callersMethodgetFragmentLengths

src/ChrCopyNumber.cpp:1110

↓ 4 callersMethodgetLevelAt

find closest value to k/ploidy for medianValue

src/ChrCopyNumber.cpp:1727

↓ 4 callersFunctiongetLine

src/myFunc.cpp:2703

↓ 4 callersMethodgetMappabilityLength

src/ChrCopyNumber.cpp:1078

↓ 4 callersMethodgetRatio

src/ChrCopyNumber.cpp:1050

↓ 4 callersMethodgetSize

src/SNPatChr.cpp:75

↓ 4 callersMethodgetSmoothedProfileAtI

src/ChrCopyNumber.cpp:1579

↓ 4 callersFunctionmatrixmatrixmultiply

src/blas.cpp:362

↓ 4 callersMethodprintCGprofile

src/GenomeCopyNumber.cpp:2890

↓ 4 callersMethodprintRatio

src/GenomeCopyNumber.cpp:1670

↓ 4 callersFunctionrmatrixblockreflector

Generate block reflector: * fill unused parts of reflectors matrix by zeros * fill diagonal of reflectors matrix by ones * generate triangular factor

src/ortfac.cpp:3093

↓ 4 callersMethodsetNormalContamination

src/ChrCopyNumber.cpp:369

↓ 4 callersMethodsetWESanalysis

src/SNPinGenome.cpp:202

↓ 4 callersFunctionstringFromBool

src/myFunc.cpp:1535

↓ 4 callersFunctionsum

src/myFunc.cpp:346

↓ 3 callersMethodaddToCoordinates

src/ChrCopyNumber.cpp:352

↓ 3 callersMethodaddToReadCount

src/ChrCopyNumber.cpp:349

↓ 3 callersFunctionbinomialcdistribution

Complemented binomial distribution Returns the sum of the terms k+1 through n of the Binomial probability density: n -- ( n ) j n-j >

src/binomialdistr.cpp:128

↓ 3 callersMethodcalculateCopyNumberMedians

src/GenomeCopyNumber.cpp:3213

↓ 3 callersMethodcalculateCopyNumberProbs_and_exomeLength

src/GenomeCopyNumber.cpp:1759

↓ 3 callersMethodcalculateCopyNumberProbs_and_genomeLength

src/GenomeCopyNumber.cpp:2122

↓ 3 callersFunctioncomplexapplyreflectionfromtheright

Application of an elementary reflection to a rectangular matrix of size MxN The algorithm post-multiplies the matrix by an elementary reflectio

src/creflections.cpp:266

↓ 3 callersMethodgetBAFProfileAt

src/ChrCopyNumber.cpp:1559

↓ 3 callersMethodgetDensityAtI

src/ChrDensity.cpp:46

↓ 3 callersMethodgetFragmentLengthsAt

src/ChrCopyNumber.cpp:1115

↓ 3 callersMethodgetGeneNameAtBin

src/ChrCopyNumber.cpp:309

↓ 3 callersFunctiongetInputFormat

src/myFunc.cpp:2666

↓ 3 callersMethodgetStatusAt

src/SNPatChr.cpp:71

↓ 3 callersMethodgetStep

src/GenomeCopyNumber.h:109

↓ 3 callersFunctionincompletegamma

Incomplete gamma integral The function is defined by x - 1 | | -t a-1

src/igammaf.cpp:59

↓ 3 callersFunctioninvnormaldistribution

Inverse of Normal distribution function Returns the argument, x, for which the area under the Gaussian probability density function (integrated from

src/normaldistr.cpp:246

↓ 3 callersFunctionmyReplace

src/myFunc.cpp:2620

↓ 3 callersMethodprintCopyNumber

src/GenomeCopyNumber.cpp:2878

↓ 3 callersMethodreadGemMappabilityFile

src/GenomeCopyNumber.cpp:2500

↓ 3 callersMethodsetGermlinePercent

src/EntryCNV.cpp:101

↓ 3 callersMethodsetMappabilityProfileAt

src/ChrCopyNumber.cpp:341

↓ 3 callersFunctiontrim

src/ConfigFile.cpp:5

↓ 2 callersFunctionEpanechnikovKernel

src/KernelVector.cpp:62

↓ 2 callersFunctionablasmicroblocksize

Microblock size -- ALGLIB routine -- 15.12.2009 Bochkanov Sergey ************************************************************************

src/ablas.cpp:228

↓ 2 callersMethodaddToEnds

src/ChrCopyNumber.cpp:356

↓ 2 callersFunctionbidiagonalsvddecompositioninternal

Internal working subroutine for bidiagonal decomposition *************************************************************************/

src/bdsvd.cpp:185

↓ 2 callersMethodcalculateBAFBreakpoints

src/ChrCopyNumber.cpp:692

↓ 2 callersMethodcalculateBreakpoints

src/ChrCopyNumber.cpp:687

↓ 2 callersFunctioncalculateBreakpoints_general

src/myFunc.cpp:714

↓ 2 callersMethodcalculateRatio

src/GenomeCopyNumber.cpp:1312

↓ 2 callersMethodcalculateRatio

src/ChrCopyNumber.cpp:462

↓ 2 callersMethodcalculateRatioLog

src/ChrCopyNumber.cpp:441

↓ 2 callersFunctioncalculatemoments

Calculation of the distribution moments: mean, variance, slewness, kurtosis. Input parameters: X - sample. Array with whose indexes range

src/descriptivestatistics.cpp:42

↓ 2 callersFunctioncomplement

src/myFunc.cpp:1849

↓ 2 callersFunctioncopyandtranspose

src/blas.cpp:215

↓ 2 callersFunctioncopymatrix

src/blas.cpp:156

↓ 2 callersFunctiondeleteChar

src/myFunc.cpp:1800

↓ 2 callersFunctionerf

Error function The integral is x - 2 | | 2 erf(x) = ------

src/normaldistr.cpp:56

↓ 2 callersFunctionexpm1

src/myFunc.cpp:2630

↓ 2 callersFunctionfactorial

src/myFunc.cpp:534

↓ 2 callersMethodfillCGprofile

src/ChrCopyNumber.cpp:1421

↓ 2 callersMethodfindIndex

src/SNPinGenome.cpp:459

↓ 2 callersMethodfindIndex

src/GenomeCopyNumber.cpp:420

↓ 2 callersFunctionfindnextbreakpoint

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function that finds the next breakpoint in the segment x:

src/myFunc.cpp:625

↓ 2 callersFunctiongammastirf

src/gammafunc.cpp:303

↓ 2 callersMethodgetArg

src/ThreadPool.h:132

↓ 2 callersMethodgetBreakPoints

src/ChrCopyNumber.cpp:1123

↓ 2 callersMethodgetCoverageAtI

src/ChrDensity.cpp:38

↓ 2 callersMethodgetEnd

src/EntryCNV.cpp:90

↓ 2 callersMethodgetEstimatedBAFuncertaintyAtBin

src/ChrCopyNumber.cpp:1091

↓ 2 callersMethodgetEstimatedBAFuncertaintyAtI

src/ChrCopyNumber.cpp:1571

↓ 2 callersMethodgetMedianValuesAt

src/ChrCopyNumber.cpp:1035

↓ 2 callersFunctiongetNormalBAFforPloidy

src/myFunc.cpp:2447

↓ 2 callersMethodgetNormalNumberOfPairs

src/GenomeCopyNumber.cpp:74

↓ 2 callersMethodgetNucleotideAt

src/SNPatChr.cpp:55

↓ 2 callersFunctiongetSAMinfo

src/myFunc.cpp:2508

↓ 2 callersMethodgetSNPChr

src/SNPinGenome.h:35

↓ 2 callersMethodgetStart

src/EntryCNV.cpp:87

↓ 2 callersFunctiongetXYBAFforPloidy

src/myFunc.cpp:2464

↓ 2 callersFunctionget_iqr

Calculate inter quartile range across individuals ---------------------------------------------------------------------------

src/myFunc.cpp:226

↓ 2 callersFunctionget_max_index

This function returns the index of the maximum value in the vector 'data'. When there are several equal maximum elements then the lowest index is retu

src/myFunc.cpp:543

↓ 2 callersMethodgetcontent

↓ 2 callersFunctionhermitianmatrixvectormultiply

src/hblas.cpp:30

↓ 2 callersFunctionhermitianrank2update

src/hblas.cpp:128

↓ 2 callersFunctionincompletebetaps

Power series for incomplete beta integral. Use when b*x is small and x not too close to 1. Cephes Math Library, Release 2.8: June, 2000 Copyright 19

src/ibetaf.cpp:894

↓ 2 callersFunctionint2string

src/myFunc.cpp:1793

↓ 2 callersFunctioninvincompletebeta

Inverse of imcomplete beta integral Given y, the function finds x such that incbet( a, b, x ) = y . The routine performs interval halving or Newto

src/ibetaf.cpp:238

↓ 2 callersFunctioninvincompletegammac

Inverse of complemented imcomplete gamma integral Given p, the function finds x such that igamc( a, x ) = p. Starting with the approximate value

src/igammaf.cpp:257

↓ 2 callersFunctionisCG

src/myFunc.cpp:1364

↓ 2 callersFunctionisN

src/myFunc.cpp:1371

↓ 2 callersFunctionlog1p

src/myFunc.cpp:2636

↓ 2 callersFunctionlrinternal

Internal linear regression subroutine *************************************************************************/

src/linreg.cpp:807

↓ 2 callersMethodnextNoNAIndex

src/ChrCopyNumber.cpp:1131

↓ 2 callersMethodprintBAF

src/GenomeCopyNumber.cpp:1718

↓ 2 callersMethodprintCNVs

src/GenomeCopyNumber.cpp:2921

↓ 2 callersMethodprintEntryCNV

src/EntryCNV.cpp:56

↓ 2 callersMethodpush_SNP

src/SNPatChr.cpp:39

↓ 2 callersMethodreadCGprofile

src/GenomeCopyNumber.cpp:2642

↓ 2 callersMethodreadMateFile

src/SNPinGenome.cpp:185

↓ 2 callersMethodreadSNPs

src/SNPinGenome.cpp:80

↓ 2 callersMethodrecalcFlanks

src/ChrCopyNumber.cpp:1278

↓ 2 callersMethodrecalculateRatio

src/ChrCopyNumber.cpp:485

↓ 2 callersMethodrecalculateRatioWithContam

src/ChrCopyNumber.cpp:660

↓ 2 callersFunctionrmatrixbdmultiplybyp

Multiplication by matrix P which reduces matrix A to bidiagonal form. The algorithm allows pre- or post-multiply by P or P'. Input parameters:

src/ortfac.cpp:1863

↓ 2 callersFunctionrmatrixbdmultiplybyq

Multiplication by matrix Q which reduces matrix A to bidiagonal form. The algorithm allows pre- or post-multiply by Q or Q'. Input parameters:

src/ortfac.cpp:1638

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