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Functions640 in github.com/BoevaLab/FREEC

⨍ Functions 640◇ Types & classes 40

↓ 202 callersMethodcompare

src/EntryCNV.cpp:109

↓ 139 callersMethodgetChromosome

src/ChrCopyNumber.cpp:1083

↓ 130 callersFunctionvmove

↓ 125 callersMethodgetstride

↓ 96 callersMethodsetlength

↓ 75 callersMethodsetbounds

↓ 60 callersMethodgetCoordinateAtBin

src/ChrCopyNumber.cpp:320

↓ 50 callersFunctionvadd

↓ 49 callersFunctionround_f

src/myFunc.cpp:1339

↓ 46 callersMethodGetLength

↓ 44 callersFunctionvdotproduct

↓ 44 callersFunctionvmul

↓ 43 callersMethodGetStep

↓ 43 callersMethodgetLength

src/ChrDensity.cpp:34

↓ 42 callersFunctionsplit

src/myFunc.cpp:47

↓ 41 callersFunctionablasblocksize

Returns block size - subdivision size where cache-oblivious soubroutines switch to the optimized kernel. INPUT PARAMETERS A - real matrix,

src/ablas.cpp:196

↓ 40 callersFunctionablascomplexblocksize

Block size for complex subroutines. -- ALGLIB routine -- 15.12.2009 Bochkanov Sergey ****************************************************

src/ablas.cpp:212

↓ 33 callersMethodgetValueAt

src/SNPatChr.cpp:67

↓ 30 callersMethodGetData

↓ 28 callersMethodgetEndAtBin

src/ChrCopyNumber.cpp:323

↓ 27 callersFunctionvsub

↓ 24 callersFunctioncmatrixgemm

This subroutine calculates C = alpha*op1(A)*op2(B) +beta*C where: * C is MxN general matrix * op1(A) is MxK matrix * op2(B) is KxN matrix * "op" may b

src/ablas.cpp:1417

↓ 24 callersFunctionrmatrixgemm

Same as CMatrixGEMM, but for real numbers. OpType may be only 0 or 1. -- ALGLIB routine -- 16.12.2009 Bochkanov Sergey ******************

src/ablas.cpp:1521

↓ 23 callersFunctionprocessChrName

src/myFunc.cpp:1730

↓ 21 callersFunctionalglib_align

src/ialglib.cpp:19

↓ 20 callersFunctionget_median

Calculate median across individuals ---------------------------------------------------------------------------

src/myFunc.cpp:123

↓ 18 callersFunctionextsignbdsqr

src/bdsvd.cpp:1026

↓ 18 callersMethodgetRatioAtBin

src/ChrCopyNumber.cpp:1087

↓ 17 callersMethodaddThread

src/ThreadPool.h:159

↓ 16 callersMethodgetCGprofileAt

src/ChrCopyNumber.cpp:1039

↓ 16 callersMethodgetChrLength

src/ChrCopyNumber.cpp:1073

↓ 16 callersMethodmappedPlusOneAtI

src/ChrCopyNumber.cpp:252

↓ 15 callersMethodhasValue

src/ConfigFile.cpp:87

↓ 13 callersMethodgetValueAt

src/ChrCopyNumber.cpp:316

↓ 12 callersFunctionapplyreflectionfromtheleft

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

src/reflections.cpp:188

↓ 12 callersMethodgetChrCopyNumber

src/GenomeCopyNumber.cpp:1665

↓ 12 callersFunctionlngamma

Natural logarithm of gamma function Input parameters: X - argument Result: logarithm of the absolute value of the Gamma(X). Output

src/gammafunc.cpp:181

↓ 11 callersFunctionablascomplexsplitlength

Complex ABLASSplitLength -- ALGLIB routine -- 15.12.2009 Bochkanov Sergey ***************************************************************

src/ablas.cpp:166

↓ 11 callersFunctionablassplitlength

Splits matrix length in two parts, left part should match ABLAS block size INPUT PARAMETERS A - real matrix, is passed to ensure that we didn

src/ablas.cpp:145

↓ 11 callersFunctionapplyreflectionfromtheright

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

src/reflections.cpp:259

↓ 11 callersMethodcalculateRatioUsingCG

src/GenomeCopyNumber.cpp:568

↓ 11 callersMethodgetExons_Countchr

src/ChrCopyNumber.cpp:330

↓ 11 callersFunctionstrccnt

src/myFunc.cpp:1756

↓ 10 callersMethodgetBAFsymbolAt

src/ChrCopyNumber.cpp:1567

↓ 10 callersMethodgetEndsSize

src/ChrCopyNumber.cpp:1592

↓ 10 callersFunctionlrunpack

Unpacks coefficients of linear model. INPUT PARAMETERS: LM - linear model in ALGLIB format OUTPUT PARAMETERS: V - coe

src/linreg.cpp:406

↓ 10 callersFunctionpolynomial

src/myFunc.cpp:1381

↓ 10 callersMethodrecalculateRatio

src/GenomeCopyNumber.cpp:425

↓ 10 callersMethodunlock

src/ThreadPool.cpp:36

↓ 9 callersFunctionapplyrotationsfromtheleft

Application of a sequence of elementary rotations to a matrix The algorithm pre-multiplies the matrix by a sequence of rotation transformations whic

src/rotations.cpp:55

↓ 9 callersFunctiongeneratereflection

Generation of an elementary reflection transformation The subroutine generates elementary reflection H of order N, so that, for a given X, the follow

src/reflections.cpp:68

↓ 9 callersFunctiongeneraterotation

The subroutine generates the elementary rotation, so that: [ CS SN ] . [ F ] = [ R ] [ -SN CS ] [ G ] [ 0 ] CS**2 + SN**2 = 1 *****

src/rotations.cpp:306

↓ 9 callersMethodgetMedianProfileAtI

src/ChrCopyNumber.cpp:1032

↓ 9 callersMethodgetNotNprofileAt

src/ChrCopyNumber.cpp:1042

↓ 9 callersFunctionlrbuild

Linear regression Subroutine builds model: Y = A(0)*X[0] + ... + A(N-1)*X[N-1] + A(N) and model found in ALGLIB format, covariation matrix, tra

src/linreg.cpp:70

↓ 9 callersFunctionlrbuildz

Like LRBuild but builds model Y = A(0)*X[0] + ... + A(N-1)*X[N-1] i.e. with zero constant term. -- ALGLIB -- Copyright 30.10.2008 by Boc

src/linreg.cpp:358

↓ 9 callersFunctionrmatrixbdsvd

Singular value decomposition of a bidiagonal matrix (extended algorithm) The algorithm performs the singular value decomposition of a bidiagonal m

src/bdsvd.cpp:134

↓ 8 callersMethodgetMappabilityProfileAt

src/ChrCopyNumber.cpp:1046

↓ 8 callersFunctionincompletebeta

Incomplete beta integral Returns incomplete beta integral of the arguments, evaluated from zero to x. The function is defined as x

src/ibetaf.cpp:84

↓ 8 callersMethodpushSmoothedProfile

src/ChrCopyNumber.cpp:1588

↓ 8 callersMethodreadCopyNumber

src/GenomeCopyNumber.cpp:42

↓ 7 callersMethodgetLength

src/ChrCopyNumber.cpp:1070

↓ 7 callersFunctiongetMateOrientation

src/myFunc.cpp:2644

↓ 7 callersFunctionincompletegammac

Complemented incomplete gamma integral The function is defined by igamc(a,x) = 1 - igam(a,x) inf.

src/igammaf.cpp:135

↓ 7 callersFunctioninplacetranspose

src/blas.cpp:184

↓ 7 callersFunctionround_by_ploidy

find closest value to k/ploidy for medianValue

src/myFunc.cpp:1333

↓ 7 callersMethodrun

src/ThreadPool.cpp:76

↓ 7 callersFunctionusage

src/Help.cpp:24

↓ 6 callersFunctionNormalDistributionDensity

src/myFunc.cpp:2384

↓ 6 callersFunctionadvance_to

src/myFunc.cpp:457

↓ 6 callersFunctioncmatrixcopy

Copy Input parameters: M - number of rows N - number of columns A - source matrix, MxN submatrix is copied and transposed

src/ablas.cpp:368

↓ 6 callersFunctiongamma

Gamma function Input parameters: X - argument Domain: 0 < X < 171.6 -170 < X < 0, X is not an integer. Relative error: arithmetic

src/gammafunc.cpp:52

↓ 6 callersMethodgetMedianValues

src/ChrCopyNumber.cpp:1099

↓ 6 callersMethodgetPositionAt

src/SNPatChr.cpp:51

↓ 6 callersMethodgetValues

src/ChrCopyNumber.cpp:397

↓ 6 callersMethodlock

src/ThreadPool.cpp:31

↓ 6 callersMethodnewThreadPool

src/ThreadPool.cpp:26

↓ 6 callersFunctionreadFileWithGenomeInfo

src/myFunc.cpp:299

↓ 6 callersFunctionrmatrixbd

Reduction of a rectangular matrix to bidiagonal form The algorithm reduces the rectangular matrix A to bidiagonal form by orthogonal transformation

src/ortfac.cpp:1413

↓ 6 callersFunctionrmatrixbdunpackdiagonals

Unpacking of the main and secondary diagonals of bidiagonal decomposition of matrix A. Input parameters: B - output of RMatrixBD subroutine.

src/ortfac.cpp:2016

↓ 6 callersFunctionrmatrixcopy

Copy Input parameters: M - number of rows N - number of columns A - source matrix, MxN submatrix is copied and transposed

src/ablas.cpp:399

↓ 6 callersFunctionrunEM

src/myFunc.cpp:1463

↓ 5 callersFunctionapplyrotationsfromtheright

Application of a sequence of elementary rotations to a matrix The algorithm post-multiplies the matrix by a sequence of rotation transformations whi

src/rotations.cpp:191

↓ 5 callersFunctioncomplexapplyreflectionfromtheleft

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

src/creflections.cpp:195

↓ 5 callersMethodgetChr

src/EntryCNV.cpp:78

↓ 5 callersMethodgetK

src/KernelVector.cpp:40

↓ 5 callersMethodgetWindowSize

src/GenomeCopyNumber.cpp:78

↓ 5 callersFunctionget_min_index

This function returns the index of the minimum value in the vector v. When there are several equal minimum elements then the lowest index is returned.

src/myFunc.cpp:557

↓ 5 callersMethodisMedianCalculated

src/ChrCopyNumber.cpp:1053

↓ 5 callersMethodisSmoothed

src/ChrCopyNumber.cpp:1056

↓ 5 callersFunctionrmatrixbdunpackpt

Unpacking matrix P which reduces matrix A to bidiagonal form. The subroutine returns transposed matrix P. Input parameters: QP - matrices

src/ortfac.cpp:1790

↓ 5 callersFunctionrmatrixbdunpackq

Unpacking matrix Q which reduces a matrix to bidiagonal form. Input parameters: QP - matrices Q and P in compact form.

src/ortfac.cpp:1565

↓ 5 callersFunctionsd

This function evaluate standard diviation supposing that E(a) = b.

src/myFunc.cpp:610

↓ 4 callersFunctionablasinternalsplitlength

Complex ABLASSplitLength -- ALGLIB routine -- 15.12.2009 Bochkanov Sergey ***************************************************************

src/ablas.cpp:1625

↓ 4 callersFunctioncmatrixblockreflector

Generate block reflector (complex): * fill unused parts of reflectors matrix by zeros * fill diagonal of reflectors matrix by ones * generate triangul

src/ortfac.cpp:3202

↓ 4 callersFunctioncomplexgeneratereflection

Generation of an elementary complex reflection transformation The subroutine generates elementary complex reflection H of order N, so that, for a

src/creflections.cpp:66

↓ 4 callersMethodfocusOnCapture

src/GenomeCopyNumber.cpp:4199

↓ 4 callersMethodgetBAFsymbPerFrg

src/ChrCopyNumber.cpp:1095

↓ 4 callersMethodgetCopyNumber

src/EntryCNV.cpp:93

↓ 4 callersMethodgetFlags

src/ThreadPool.h:52

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