libStatGen Software  1
Pedigree Class Reference
Inheritance diagram for Pedigree:
Collaboration diagram for Pedigree:

Public Member Functions

void Prepare (IFILE &input)
 
void Load (IFILE &input)
 
void LoadMendel (IFILE &input)
 
void Prepare (const char *input)
 
void Load (const char *input, bool allowFailures=false)
 
int TranslateSexCode (const char *code, bool &failure)
 
void PrepareDichotomization ()
 
int Dichotomize (int trait, double mean=_NAN_)
 
void DichotomizeAll (double mean=_NAN_)
 
void WriteDataFile (FILE *output)
 
void WritePedigreeFile (FILE *output)
 
void WriteDataFile (const char *output)
 
void WritePedigreeFile (const char *output)
 
void WritePerson (FILE *output, int who, const char *famid=NULL, const char *pid=NULL, const char *fatid=NULL, const char *motid=NULL)
 
void WriteRecodedPerson (FILE *output, int who, MarkerInfo **markerInfo, const char *famid=NULL, const char *pid=NULL, const char *fatid=NULL, const char *motid=NULL)
 
void Sort ()
 
FamilyFindFamily (const char *famid)
 
PersonFindPerson (const char *famid, const char *pid)
 
int CountAlleles (int marker)
 
void LumpAlleles (double treshold, bool reorder=true)
 
void EstimateFrequencies (int estimator, bool quiet=false)
 
Personoperator[] (int i)
 
bool InheritanceCheck (bool abortIfInconsistent=true)
 
bool AutosomalCheck ()
 
bool SexLinkedCheck ()
 
bool TwinCheck ()
 
void MergeTwins ()
 
void Trim (bool quiet=false, int *informative=NULL)
 
void AddPerson (const char *famid, const char *pid, const char *fatid, const char *motid, int sex, bool delay_sort=false)
 
void ExtractFamily (int id, Pedigree &new_ped)
 
void ExtractOnAffection (int a, Pedigree &new_ped, int target_status=2)
 
void Filter (IntArray &filter)
 
void ShowMemoryInfo ()
 

Public Attributes

int size
 
int count
 
Person ** persons
 
int familyCount
 
Family ** families
 
int haveTwins
 
PedigreeDescription pd
 
PedigreeDescriptionmultiPd
 
int multiFileCount
 

Static Public Attributes

static bool sexAsCovariate = false
 
static String missing
 
- Static Public Attributes inherited from PedigreeGlobals
static int traitCount = 0
 
static int markerCount = 0
 
static int affectionCount = 0
 
static int covariateCount = 0
 
static int stringCount = 0
 
static bool chromosomeX = false
 
static bool sexSpecificMap = false
 
static StringArray traitNames
 
static StringArray covariateNames
 
static StringArray affectionNames
 
static StringArray markerNames
 
static StringArray stringNames
 
static StringIntHash markerLookup
 
static StringIntHash traitLookup
 
static StringIntHash affectionLookup
 
static StringIntHash covariateLookup
 
static StringIntHash stringLookup
 
static int markerInfoCount = 0
 
static int markerInfoSize = 0
 
static MarkerInfo ** markerInfo = NULL
 
static StringHash markerInfoByName
 
static MarkerInfo ** markerInfoByInteger = NULL
 

Additional Inherited Members

- Static Public Member Functions inherited from PedigreeGlobals
static int GetTraitID (const char *name)
 
static int GetMarkerID (const char *name)
 
static int GetCovariateID (const char *name)
 
static int GetAffectionID (const char *name)
 
static int GetStringID (const char *name)
 
static int LookupTrait (const char *name)
 
static int LookupMarker (const char *name)
 
static int LookupCovariate (const char *name)
 
static int LookupAffection (const char *name)
 
static int LookupString (const char *name)
 
static void GrowMarkerInfo ()
 
static MarkerInfoGetMarkerInfo (String &name)
 
static MarkerInfoGetMarkerInfo (int marker)
 
static int SortMarkersInMapOrder (IntArray &markers, int chromosome=-1)
 
static void GetOrderedMarkers (IntArray &markers)
 
static void FlagMissingMarkers (IntArray &missingMarkers)
 
static bool MarkerPositionsAvailable ()
 
static bool AlleleFrequenciesAvailable ()
 
static void VerifySexSpecificOrder ()
 
static void LoadAlleleFrequencies (const char *filename, bool required=false)
 
static void LoadAlleleFrequencies (IFILE &file)
 
static void LoadMarkerMap (const char *filename, bool filter=false)
 
static void LoadMarkerMap (IFILE &file, bool filter=false)
 
static void LoadBasepairMap (const char *filename)
 
static void LoadBasepairMap (IFILE &file)
 
static void WriteMapFile (const char *filename)
 
static void WriteMapFile (FILE *file)
 
static void WriteFreqFile (const char *filename, bool old_format=false)
 
static void WriteFreqFile (FILE *file, bool old_format=false)
 
static int LoadAllele (int marker, String &label)
 
static int LoadAllele (MarkerInfo *info, String &label)
 

Detailed Description

Definition at line 32 of file Pedigree.h.


The documentation for this class was generated from the following files: