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void | Prepare (IFILE &input) |
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void | Load (IFILE &input) |
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void | LoadMendel (IFILE &input) |
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void | Prepare (const char *input) |
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void | Load (const char *input, bool allowFailures=false) |
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int | TranslateSexCode (const char *code, bool &failure) |
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void | PrepareDichotomization () |
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int | Dichotomize (int trait, double mean=_NAN_) |
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void | DichotomizeAll (double mean=_NAN_) |
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void | WriteDataFile (FILE *output) |
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void | WritePedigreeFile (FILE *output) |
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void | WriteDataFile (const char *output) |
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void | WritePedigreeFile (const char *output) |
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void | WritePerson (FILE *output, int who, const char *famid=NULL, const char *pid=NULL, const char *fatid=NULL, const char *motid=NULL) |
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void | WriteRecodedPerson (FILE *output, int who, MarkerInfo **markerInfo, const char *famid=NULL, const char *pid=NULL, const char *fatid=NULL, const char *motid=NULL) |
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void | Sort () |
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Family * | FindFamily (const char *famid) |
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Person * | FindPerson (const char *famid, const char *pid) |
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int | CountAlleles (int marker) |
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void | LumpAlleles (double treshold, bool reorder=true) |
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void | EstimateFrequencies (int estimator, bool quiet=false) |
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Person & | operator[] (int i) |
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bool | InheritanceCheck (bool abortIfInconsistent=true) |
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bool | AutosomalCheck () |
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bool | SexLinkedCheck () |
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bool | TwinCheck () |
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void | MergeTwins () |
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void | Trim (bool quiet=false, int *informative=NULL) |
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void | AddPerson (const char *famid, const char *pid, const char *fatid, const char *motid, int sex, bool delay_sort=false) |
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void | ExtractFamily (int id, Pedigree &new_ped) |
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void | ExtractOnAffection (int a, Pedigree &new_ped, int target_status=2) |
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void | Filter (IntArray &filter) |
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void | ShowMemoryInfo () |
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static int | GetTraitID (const char *name) |
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static int | GetMarkerID (const char *name) |
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static int | GetCovariateID (const char *name) |
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static int | GetAffectionID (const char *name) |
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static int | GetStringID (const char *name) |
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static int | LookupTrait (const char *name) |
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static int | LookupMarker (const char *name) |
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static int | LookupCovariate (const char *name) |
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static int | LookupAffection (const char *name) |
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static int | LookupString (const char *name) |
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static void | GrowMarkerInfo () |
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static MarkerInfo * | GetMarkerInfo (String &name) |
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static MarkerInfo * | GetMarkerInfo (int marker) |
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static int | SortMarkersInMapOrder (IntArray &markers, int chromosome=-1) |
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static void | GetOrderedMarkers (IntArray &markers) |
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static void | FlagMissingMarkers (IntArray &missingMarkers) |
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static bool | MarkerPositionsAvailable () |
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static bool | AlleleFrequenciesAvailable () |
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static void | VerifySexSpecificOrder () |
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static void | LoadAlleleFrequencies (const char *filename, bool required=false) |
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static void | LoadAlleleFrequencies (IFILE &file) |
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static void | LoadMarkerMap (const char *filename, bool filter=false) |
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static void | LoadMarkerMap (IFILE &file, bool filter=false) |
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static void | LoadBasepairMap (const char *filename) |
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static void | LoadBasepairMap (IFILE &file) |
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static void | WriteMapFile (const char *filename) |
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static void | WriteMapFile (FILE *file) |
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static void | WriteFreqFile (const char *filename, bool old_format=false) |
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static void | WriteFreqFile (FILE *file, bool old_format=false) |
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static int | LoadAllele (int marker, String &label) |
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static int | LoadAllele (MarkerInfo *info, String &label) |
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Definition at line 32 of file Pedigree.h.