Functions — github.com/BoevaLab/FREEC

CodeHub MCPcopy Create free account

hub / github.com/BoevaLab/FREEC / functions

Functions640 in github.com/BoevaLab/FREEC

⨍ Functions 640◇ Types & classes 40

↓ 1 callersMethodgetWESanalysis

src/GenomeCopyNumber.cpp:4309

↓ 1 callersFunctionget_conf_file

src/main.cpp:49

↓ 1 callersFunctionget_mean

Calculate mean across individuals ---------------------------------------------------------------------------

src/myFunc.cpp:197

↓ 1 callersFunctionget_medianNotNA

src/myFunc.cpp:137

↓ 1 callersFunctionget_sd

Calculate sd across individuals around given mean ---------------------------------------------------------------------------

src/myFunc.cpp:156

↓ 1 callersFunctionget_weighted_mean

Calculate weighted mean across individuals ---------------------------------------------------------------------------

src/myFunc.cpp:208

↓ 1 callersMethodifHasRatio

src/ChrCopyNumber.cpp:643

↓ 1 callersFunctionincompletebetafe

Continued fraction expansion #1 for incomplete beta integral Cephes Math Library, Release 2.8: June, 2000 Copyright 1984, 1995, 2000 by Stephen L. M

src/ibetaf.cpp:664

↓ 1 callersFunctionincompletebetafe2

Continued fraction expansion #2 for incomplete beta integral Cephes Math Library, Release 2.8: June, 2000 Copyright 1984, 1995, 2000 by Stephen L. M

src/ibetaf.cpp:778

↓ 1 callersMethodinitCopyNumber

src/GenomeCopyNumber.cpp:175

↓ 1 callersFunctioninternalstatheapsort

src/descriptivestatistics.cpp:347

↓ 1 callersMethodisMappUsed

src/GenomeCopyNumber.cpp:40

↓ 1 callersFunctionlravgerror

Average error on the test set INPUT PARAMETERS: LM - linear model XY - test set NPoints - test set size RESULT: aver

src/linreg.cpp:528

↓ 1 callersFunctionlravgrelerror

RMS error on the test set INPUT PARAMETERS: LM - linear model XY - test set NPoints - test set size RESULT: average

src/linreg.cpp:567

↓ 1 callersFunctionlrbuilds

Linear regression Variant of LRBuild which uses vector of standatd deviations (errors in function values). INPUT PARAMETERS: XY - tra

src/linreg.cpp:134

↓ 1 callersFunctionlrbuildzs

Like LRBuildS, 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 B

src/linreg.cpp:244

↓ 1 callersFunctionlrlines

src/linreg.cpp:668

↓ 1 callersFunctionlrrmserror

RMS error on the test set INPUT PARAMETERS: LM - linear model XY - test set NPoints - test set size RESULT: root mea

src/linreg.cpp:489

↓ 1 callersMethodmakepileup

src/BAFpileup.cpp:31

↓ 1 callersFunctionmerge_no_dups

src/myFunc.h:165

↓ 1 callersFunctionpathAppend

src/myFunc.cpp:1347

↓ 1 callersMethodperform

src/SNPinGenome.cpp:209

↓ 1 callersMethodprintInfo

src/GenomeCopyNumber.cpp:2915

↓ 1 callersFunctionprint_version

src/main.cpp:42

↓ 1 callersFunctionreadChrNamesInBed

src/myFunc.cpp:267

↓ 1 callersMethodrecalculateLogRatio

src/ChrCopyNumber.cpp:654

↓ 1 callersMethodrecalculateRatioUsingCG

src/GenomeCopyNumber.cpp:442

↓ 1 callersMethodreleaseOneThread

src/ThreadPool.cpp:53

↓ 1 callersMethodremoveLargeExons

src/ChrCopyNumber.cpp:1267

↓ 1 callersMethodremoveLowReadCountWindows

src/GenomeCopyNumber.cpp:1113

↓ 1 callersMethodremoveLowReadCountWindows

src/ChrCopyNumber.cpp:402

↓ 1 callersMethodremoveLowReadCountWindowsFromControl

src/GenomeCopyNumber.cpp:1121

↓ 1 callersMethodreserveOneThread

src/ThreadPool.cpp:41

↓ 1 callersFunctionrmatrixgemmf

Fast kernel -- ALGLIB routine -- 19.01.2010 Bochkanov Sergey *************************************************************************/

src/ablasf.cpp:319

↓ 1 callersFunctionrmatrixgemmk

GEMM kernel -- ALGLIB routine -- 16.12.2009 Bochkanov Sergey *************************************************************************/

src/ablas.cpp:2926

↓ 1 callersFunctionrmatrixlefttrsm2

Level 2 subroutine *************************************************************************/

src/ablas.cpp:2259

↓ 1 callersFunctionrmatrixlefttrsmf

Fast kernel -- ALGLIB routine -- 19.01.2010 Bochkanov Sergey *************************************************************************/

src/ablasf.cpp:227

↓ 1 callersFunctionrmatrixlqbasecase

Base case for real LQ -- LAPACK routine (version 3.0) -- Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., Courant Institute, A

src/ortfac.cpp:2918

↓ 1 callersFunctionrmatrixlqunpackq

Partial unpacking of matrix Q from the LQ decomposition of a matrix A Input parameters: A - matrices L and Q in compact form.

src/ortfac.cpp:820

↓ 1 callersFunctionrmatrixmvf

Fast kernel -- ALGLIB routine -- 19.01.2010 Bochkanov Sergey *************************************************************************/

src/ablasf.cpp:112

↓ 1 callersFunctionrmatrixqrbasecase

Base case for real QR -- LAPACK routine (version 3.0) -- Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., Courant Institute, A

src/ortfac.cpp:2867

↓ 1 callersFunctionrmatrixqrunpackq

Partial unpacking of matrix Q from the QR decomposition of a matrix A Input parameters: A - matrices Q and R in compact form.

src/ortfac.cpp:636

↓ 1 callersFunctionrmatrixrank1f

Fast kernel -- ALGLIB routine -- 19.01.2010 Bochkanov Sergey *************************************************************************/

src/ablasf.cpp:59

↓ 1 callersFunctionrmatrixrighttrsm2

Level 2 subroutine -- ALGLIB routine -- 15.12.2009 Bochkanov Sergey *********************************************************************

src/ablas.cpp:2096

↓ 1 callersFunctionrmatrixrighttrsmf

Fast kernel -- ALGLIB routine -- 19.01.2010 Bochkanov Sergey *************************************************************************/

src/ablasf.cpp:197

↓ 1 callersFunctionrmatrixsvd

Singular value decomposition of a rectangular matrix. The algorithm calculates the singular value decomposition of a matrix of size MxN: A = U * S *

↓ 1 callersFunctionrmatrixsyrk2

Level 2 subrotuine *************************************************************************/

src/ablas.cpp:2547

↓ 1 callersFunctionrmatrixsyrkf

Fast kernel -- ALGLIB routine -- 19.01.2010 Bochkanov Sergey *************************************************************************/

src/ablasf.cpp:288

↓ 1 callersFunctionrunEMlog

src/myFunc.cpp:1636

↓ 1 callersMethodrunning

src/ThreadPool.h:86

↓ 1 callersMethodsetAllNormal

src/ChrCopyNumber.cpp:544

↓ 1 callersMethodsetBin

src/SNPposition.cpp:99

↓ 1 callersMethodsetBinAt

src/SNPatChr.cpp:79

↓ 1 callersMethodsetCN_subc

src/ChrCopyNumber.cpp:286

↓ 1 callersMethodsetCN_subcLength

src/ChrCopyNumber.cpp:382

↓ 1 callersMethodsetFrequency

src/SNPposition.cpp:83

↓ 1 callersMethodsetLookingForSubclones

src/ChrCopyNumber.cpp:1596

↓ 1 callersMethodsetNotNprofileAt

src/ChrCopyNumber.cpp:334

↓ 1 callersMethodsetPopulation_subc

src/ChrCopyNumber.cpp:298

↓ 1 callersMethodsetRCountToZeroForNNNN

src/ChrCopyNumber.cpp:1746

↓ 1 callersMethodsetStatus

src/SNPposition.cpp:87

↓ 1 callersMethodsetStatusAt

src/SNPatChr.cpp:63

↓ 1 callersMethodsetStep

src/ChrCopyNumber.cpp:374

↓ 1 callersMethodsetType

src/EntryCNV.cpp:105

↓ 1 callersMethodsetValueAt

src/ChrCopyNumber.cpp:283

↓ 1 callersMethodsetpop_subcLength

src/ChrCopyNumber.cpp:387

↓ 1 callersFunctionstrkeepOnly

src/myFunc.cpp:1767

↓ 1 callersFunctionsvdv2x2

src/bdsvd.cpp:1114

↓ 1 callersFunctionthread_init

src/main.cpp:157

↓ 1 callersFunctionvector_add_constant

This function adds the constant value x to the elements of the vector a, a0i = ai + x.

src/myFunc.cpp:604

↓ 1 callersFunctionvector_scale

This function multiplies the elements of vector a by the constant factor x, a0i = xai.

src/myFunc.cpp:597

↓ 1 callersFunctionvector_sub

This function subtracts the elements of vector b from the elements of vector a, a0i = ai ?�� bi. The two vectors must have the same length.

src/myFunc.cpp:587

↓ 1 callersMethodwaitFinished

src/ThreadPool.h:101

Method(*getWrapper())

src/ThreadPool.h:134

MethodBAFpileup

src/BAFpileup.cpp:26

MethodChameleon

src/Chameleon.cpp:33

MethodChameleon

src/Chameleon.h:36

MethodChrCopyNumber

src/ChrCopyNumber.cpp:26

MethodChrCopyNumberCalculateBreakpointArgWrapper

src/ChrCopyNumber.h:216

FunctionChrCopyNumber_calculateBAFBreakpoint_wrapper

src/ChrCopyNumber.cpp:1767

FunctionChrCopyNumber_calculateBreakpoint_wrapper

src/ChrCopyNumber.cpp:1757

MethodChrDensity

src/ChrDensity.cpp:26

MethodConfigFile

src/ConfigFile.cpp:19

src/EntryCNV.cpp:26

MethodEstimateSubclonalPopulation

src/SeekSubclones.cpp:197

MethodGenomeCopyNumber

src/GenomeCopyNumber.cpp:26

MethodGenomeCopyNumberCalculateBreakpointArgWrapper

src/GenomeCopyNumber.h:180

MethodGenomeCopyNumberReadMateFileArgWrapper

src/GenomeCopyNumber.h:197

FunctionGenomeCopyNumber_calculateBreakpoint_wrapper

src/GenomeCopyNumber.cpp:4348

FunctionGenomeCopyNumber_readMateFile_wrapper

src/GenomeCopyNumber.cpp:4337

MethodGenomeDensity

src/GenomeDensity.cpp:25

MethodKernelVector

src/KernelVector.cpp:25

MethodPercentageTest

src/SeekSubclones.cpp:160

src/SNPatChr.cpp:23

MethodSNPinGenome

src/SNPinGenome.cpp:26

MethodSNPinGenomePerformArgWrapper

src/SNPinGenome.h:69

FunctionSNPinGenome_perform_wrapper

src/SNPinGenome.cpp:551

MethodSNPposition

src/SNPposition.cpp:24

MethodSeekSubclones

src/SeekSubclones.cpp:26

← previous next →301–400 of 640, ranked by callers