QTLMap API

Table of Contents Sourcefiles Index QTLMap Constants Subroutines Modules Packages Types Variables

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m_qtlmap_constant

[ Top ] [ DATA ] [ Modules ]

NAME

    m_qtlmap_constant -- Definition of constantes

SYNOPSIS

    All definition useb by QTLMap are defined here....

DESCRIPTION

NOTES

SEE ALSO

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AM_MAX

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   AM_MAX

DESCRIPTION

    Maximum value for a dam qtl effect parameter for a optimization context

NOTES

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AM_MIN

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   AM_MIN

DESCRIPTION

    Minimum value for a dam qtl effect parameter for a optimization context

NOTES

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ANALYSE_2QTL_INTERACTION

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_2QTL_INTERACTION

DESCRIPTION

    Constant id 2 qtl interaction ( DEV )

NOTES

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ANALYSE_DEV_1

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_DEV_1

DESCRIPTION

   Internal ID dev of method

NOTES

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ANALYSE_DEV_2

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_DEV_2

DESCRIPTION

   Internal ID dev of method

NOTES

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ANALYSE_MULTIRAIT

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_MULTIRAIT

DESCRIPTION

   Constant id LA for a set of traits with a multivariate analysis (based on a multi­normal penetrance function)

NOTES

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ANALYSE_MULTITRAIT_DA

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_MULTITRAIT_DA

DESCRIPTION

    Constant id  LA for a set of traits (without missing data) with a discriminante analysis

NOTES

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ANALYSE_MULTITRAIT_INCIDENCE

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_MULTITRAIT_INCIDENCE

DESCRIPTION

    Constant id LA for a set of traits with a multivariate analysis with a model description (based on a multi­normal penetrance function) (multi-qtl version)
    this analysis used the structured data of m_qtlmap_incidence.F95

NOTES

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ANALYSE_MULTITRAIT_INCIDENCE_LU

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_MULTITRAIT_INCIDENCE

DESCRIPTION

    Constant id LA for a set of traits with a multivariate analysis with a model description (based on a multi­normal penetrance function) (multi-qtl version)
    this analysis used the structured data of m_qtlmap_incidence.F95

NOTES

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ANALYSE_TRAIT_COV_CONTINGENCE

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_TRAIT_COV_CONTINGENCE

DESCRIPTION

    Constant id LA for a single survey trait with a model description (other performance are treat as covariates (xiaoquiang.wang@rennes.inra.fr))
    this analysis used the structured data of m_qtlmap_incidence.F95

NOTES

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ANALYSE_UNITRAIT

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT

DESCRIPTION

   Constant id LA single trait with pre-corrected data

NOTES

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ANALYSE_UNITRAIT_CONTINGENCE

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_CONTINGENCE

DESCRIPTION

    Constant id LA for a single survey trait with a model description without interaction fixed effect - qtl (multiqtl version).
    this analysis used the structured data of m_qtlmap_incidence.F95

NOTES

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ANALYSE_UNITRAIT_LA

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_LA

DESCRIPTION

    Constant id LA for a single survey trait with the model description

NOTES

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ANALYSE_UNITRAIT_LD

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_LD

DESCRIPTION

    Constant id LD for a single data with a model description

NOTES

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ANALYSE_UNITRAIT_LDJH

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_LDJH

DESCRIPTION

    Constant id LA for a single survey trait with a model description ( DEV model LDJH )

NOTES

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ANALYSE_UNITRAIT_LDLA

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_LDLA

DESCRIPTION

    Constant id LDLA  for a single data with a model description

NOTES

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ANALYSE_UNITRAIT_LDLA_CROIS

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_LDLA_CROIS

DESCRIPTION

    Constant id LDLA  for a single data with a model description (2 breeds -->2 LD origins)

NOTES

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ANALYSE_UNITRAIT_LINEAR_LA_HETERO

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_LINEAR_LA_HETERO

DESCRIPTION

   Constant id LA for a single data with a model description (likelihood linearised ­ heteroscedastic)

NOTES

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ANALYSE_UNITRAIT_LINEAR_LA_HOMO

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_LINEAR_LA_HOMO

DESCRIPTION

   Constant id LA for a single data with a model description (likelihood linearised ­ homoscedatic)

NOTES

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ANALYSE_UNITRAIT_LINEAR_LD_HETERO

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_LINEAR_LD_HETERO

DESCRIPTION

   Constant id LD for a single data with a model description (likelihood linearised ­ heteroscedastic)

NOTES

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ANALYSE_UNITRAIT_LINEAR_LD_HOMO

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_LINEAR_LD_HOMO

DESCRIPTION

   Constant id LD  for a single data with a model description   (likelihood linearised ­ homoscedatic)

NOTES

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ANALYSE_UNITRAIT_LINEAR_LDLA_HETERO

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_LINEAR_LDLA_HETERO

DESCRIPTION

   Constant id LDLA  for a single data with a model description (likelihood linearised ­ homoscedatic)

NOTES

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ANALYSE_UNITRAIT_LINEAR_LDLA_HOMO

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_LINEAR_LDLA_HOMO

DESCRIPTION

   Constant id LDLA  for a single data with a model description (likelihood linearised ­ homoscedatic)

NOTES

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ANALYSE_UNITRAIT_MODLIN

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_MODLIN

DESCRIPTION

   Constant id LA single trait with model description

NOTES

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ANALYSE_UNITRAIT_MODLIN_COX

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ANALYSE_UNITRAIT_MODLIN_COX

DESCRIPTION

    Constant id LA for a single survey trait with the cox model

NOTES

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AP_MAX

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   AP_MIN

DESCRIPTION

    Maximum value for a sire qtl effect parameter for a optimization context

NOTES

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AP_MIN

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   AP_MIN

DESCRIPTION

    Minimum value for a sire qtl effect parameter for a optimization context

NOTES

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BC_KEYWORD

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   BC_KEYWORD

DESCRIPTION

   Backcross label in the simulation parameter file.

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COMMON_ANALYSE

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   COMMON_ANALYSE

DESCRIPTION

    Constant id for context analysis (analysis case)

NOTES

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DEFAULT_PARAM_MAX

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   DEFAULT_PARAM_MAX

DESCRIPTION

    Maximum value for a generic parameter for a optimization context

NOTES

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DEFAULT_PARAM_MIN

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   DEFAULT_PARAM_MIN

DESCRIPTION

    Minimum value for a generic parameter for a optimization context

NOTES

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DP

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   DP

DESCRIPTION

   Precision (kind) of real defined : 15 digits and exponent range greater at least 307.

NOTES

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EPS_EM

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   EPS_EM

DESCRIPTION

    maximum difference between two successive estimation of the haplotype proability
    in prob_haplo_complet

NOTES

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F2_KEYWORD

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   F2_KEYWORD

DESCRIPTION

   "F2" label in the simulation parameter file.

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FMT_INT

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   FMT_INT

DESCRIPTION

   Default Integer FMT to print in a console

NOTES

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FMT_INT_LONG

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   FMT_INT_LONG

DESCRIPTION

   Default Long Integer FMT to print in a console

NOTES

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FMT_MAX_BUFFER

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   FMT_MAX_BUFFER

DESCRIPTION

   Default maximum size of a fmt buffer string

NOTES

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FMT_REAL

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   FMT_REAL

DESCRIPTION

   Default Real FMT to print in a console

NOTES

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INIFINY_REAL_VALUE

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   INIFINY_REAL_VALUE

DESCRIPTION

   The biggest value using by the optimization package

NOTES

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INT_NOT_DEFINED

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   INT_NOT_DEFINED

DESCRIPTION

    Default initialization of integer without correct value

NOTES

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ITER_EM_MAX

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   ITER_EM_MAX

DESCRIPTION

    Maximum number of iteration in the EM in prob_haplo_complet

NOTES

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KIND_PHENO

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   KIND_PHENO

DESCRIPTION

   Precision (kind) of integer id allele defined

NOTES

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LABEL_GENEALOGY

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LABEL_GENEALOGY

DESCRIPTION

   Label genealogy description

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LABEL_MARKERS

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LABEL_MARKERS

DESCRIPTION

   Label markers description

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LABEL_NAME_TRAIT

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LABEL_NAME_TRAIT

DESCRIPTION

   Name used for each trait when a model is defined by the keyword 'all'

NOTES

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LABEL_QTL

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LABEL_QTL

DESCRIPTION

   Label QTL description

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LABEL_SIMULTRAITS

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LABEL_SIMULTRAITS

DESCRIPTION

   Label simulation phenotypic data description

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LABEL_TRAITS

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LABEL_TRAITS

DESCRIPTION

   Label phenotypic data description

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LEN_BUFFER_LINE

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LEN_BUFFER_LINE

DESCRIPTION

   Default maximum size of a buffer string line

NOTES

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LEN_BUFFER_WORD

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LEN_BUFFER_WORD

DESCRIPTION

   Default size of a buffer string

NOTES

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LEN_DEF

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LEN_DEF

DESCRIPTION

   Default size of a string

NOTES

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LEN_L

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LEN_L

DESCRIPTION

   Length size of a long word

NOTES

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LEN_LINE

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LEN_LINE

DESCRIPTION

   Maximum size length of a line readed

NOTES

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LEN_S

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LEN_S

DESCRIPTION

   Length size of a short word

NOTES

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LEN_W

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LEN_W

DESCRIPTION

   Length size of a word

NOTES

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LENGTH_MAX_FILE

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   LENGTH_MAX_FILE

DESCRIPTION

   Maximum length of a name file

NOTES

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MAX_FILES_INPUT

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   MAX_FILES_INPUT

DESCRIPTION

   Maximum files to read for input data

NOTES

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MAXNB_KEY_DEV_GEN

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   MAXNB_KEY_DEV_GEN

DESCRIPTION

   Maximum number of generic key (opt_key_dev1,opt_key_dev2,...)

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OPT_SIB_FS

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   OPT_SIB_FS

DESCRIPTION

    Definition of a constante for full sib analysis

NOTES

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OPT_SIB_HS

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   OPT_SIB_HS

DESCRIPTION

    Definition of a constante for half sib analysis

NOTES

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OUTBRED_KEYWORD

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   OUTBRED_KEYWORD

DESCRIPTION

   Outbred label in the simulation parameter file.

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REAL_NOT_DEFINED

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   REAL_NOT_DEFINED

DESCRIPTION

   Default initialization of real without correct value

NOTES

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SIG_MAX

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   SIG_MAX

DESCRIPTION

    Maximum value for a standart deviation parameter for a optimization context

NOTES

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SIG_MIN

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   SIG_MIN

DESCRIPTION

    Minimum value for a standart deviation parameter for a optimization context

NOTES

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SIMULATION

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   SIMULATION

DESCRIPTION

    Constant id for context analysis (simulation case)

NOTES

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STRING_NOT_DEFINED

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   STRING_NOT_DEFINED

DESCRIPTION

    Default initialization of string without correct value

NOTES

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TRANSCIPTOME_ANALYSE

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   TRANSCIPTOME_ANALYSE

DESCRIPTION

    Constant id for context analysis (transcriptom analysis case)

NOTES

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TYPE_DATA_CONTINUE

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   TYPE_DATA_CONTINUE

DESCRIPTION

   Constant for real data

NOTES

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TYPE_DATA_COX

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   TYPE_DATA_COX

DESCRIPTION

   Constant for model cox data

NOTES

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VAL_MAX_INDEX_PHENO

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   VAL_MAX_INDEX_PHENO

DESCRIPTION

   Maximum value of an index allele

NOTES

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VAL_MIN_INDEX_PHENO

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   VAL_MIN_INDEX_PHENO

DESCRIPTION

   Minimum value of an index allele

NOTES

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XMU_MAX

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   XMU_MAX

DESCRIPTION

    Maximum value for a mean parameter for a optimization context

NOTES

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XMU_MIN

[ Top ] [ m_qtlmap_constant ] [ Constants ]

NAME

   XMU_MIN

DESCRIPTION

    Minimum value for a mean parameter for a optimization context

NOTES

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