DATA
NAME
DATA
DESCRIPTION
Package data :
contains the module m_qtlmap_data that offers public variables of data user
(map ,genetic marker, traits, model of the traits ) and the module m_qtlmap_haplotype data generated
by the HAPLOTYPE package
m_qtlmap_data
NAME
m_qtlmap_data -- Storage of data user.
SYNOPSIS
User data are storaged in this module and
Some simples subroutines are included
DESCRIPTION
NOTES
SEE ALSO
absi
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
absi
DESCRIPTION
get abscisse in Morgan corresponding to a a position N on the chromosome CHR
alleles
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
alleles
DESCRIPTION
Get the string value of the allele referenced.
DIMENSIONS
1: chromosome index 2: marker index 3: allele index ( 1 < allele index < nall(ch,m) )
animal
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
animal
DESCRIPTION
List of the progenies
NOTES
Information from the genealogy file
BASE_STEP
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
BASE_STEP
DESCRIPTION
Morgan Base
NOTES
Information from the parameter file
bete
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
bete
DESCRIPTION
List of animal with traits
carac
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
carac
DESCRIPTION
List of traits name
cd
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
cd
DESCRIPTION
missing data or cd of index data
DIMENSIONS
1 : Trait index 2 : Phenotyped animal referenced in bete
ch
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
ch
DESCRIPTION
Name of the chromosome
NOTES
ch(1) => name of the fisrt chromosome
...
Information from the map file (rec=2)
chromo
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
chromo
DESCRIPTION
List of chromosome name
NOTES
Information from the map file
corperf
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
corperf
DESCRIPTION
Contains the corresponding index of y from an index animal
DIMENSIONS
1: animal id referenced in animal
NOTES
indBete = corperf(idanimal) => y(1,indBete) is the first trait of the animal animal(indanimal)
corred
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
corred
DESCRIPTION
Contains the corresponding numero index from an animal index
NOTES
numeroIndex = corred(indanaimal) => numero(numeroIndex) == animal(indanimal) size(corred) = nd
corregm
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
corregm
DESCRIPTION
Contains the corresponding numero index from a gmere index
NOTES
numeroIndex = corregm(indgmere) => numero(numeroIndex) == gmere(indgmere) size(corregm) = ngm
corregp
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
corregp
DESCRIPTION
Contains the corresponding numro index from a gpere index
NOTES
numeroIndex = corregp(indgpere) => numero(numeroIndex) == gpere(indgpere) size(corregp) = ngp
correm
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
correm
DESCRIPTION
Contains the corresponding numero index from a dam index
NOTES
numeroIndex = correm(indmere) => numero(numeroIndex) == mere(indmere) size(correm) = nm
correp
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
correp
DESCRIPTION
Contains the corresponding numero index from a sire index
NOTES
numeroIndex = correp(indpere) => numero(numeroIndex) == pere(indpere) size(correp) = np
correr
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
correr
DESCRIPTION
Contains the corresponding numero index from a reproductor index
NOTES
numeroIndex = correr(indrepro) => numero(numeroIndex) == repro(indrepro) size(correr) = nr
covar
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
covar
DESCRIPTION
Index value of the covariate for each animal DIMENSIONS: 1: animal index 2: covariate index
EPS_LINEAR_HETEROSCEDASTIC
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
EPS_LINEAR_HETEROSCEDASTIC
DESCRIPTION
Threshold for convergence in the linear mode heteroscedastic
NOTES
Information from the parameter file
estfem
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
estfem
DESCRIPTION
Estimability per progeny genotyped
DIMENSIONS
1: trait index 2: female index
NOTES
size(2,estime) == size(mere)
estime
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
estime
DESCRIPTION
Estimability per progeny phenotyped
DIMENSIONS
1: trait index 2: dam index
NOTES
size(2,estime) == size(mere)
femelle
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
female
DESCRIPTION
List of female id : a sub set of mere. contains single id
NOTES
geneaFileDefined
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
geneaFileDefined
DESCRIPTION
flag to test if a user genealogy file existe
genotypeFileDefined
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
genotypeFileDefined
DESCRIPTION
flag to test if a user genotype file existe
gmere
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
gmere
DESCRIPTION
List of the grand dam name
gpere
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
gpere
DESCRIPTION
List of the grand sire name
NOTES
Information from the genealogy file
h2
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
h2
DESCRIPTION
heritabilities of traits , dim : ncar
DIMENSIONS
1 : Trait index
iam
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
iam
DESCRIPTION
Indexe of the female
DIMENSIONS
1: trait index 2: female index
NOTES
iam(ifem) = indam : 0<= indam <= namest
in_carte
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
carte
DESCRIPTION
File map name
in_genea
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
in_genea
DESCRIPTION
Genealogy file name.
in_param_ef
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
param_ef
DESCRIPTION
Model files describing fixed effect, covariate, interaction fixed effect and qtl for each traits
NOTES
in_parsim
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
parsim
DESCRIPTION
simulation user file
in_perfs
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
perfs
DESCRIPTION
Phenotypic records user files / traits data
DIMENSIONS
MAX_FILES_INPUT
NOTES
in_race
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
in_race
DESCRIPTION
breed file name.
in_typage
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
typage
DESCRIPTION
Genotype records user files
indicemod
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
indicemod
DESCRIPTION
Correspond value from a original discrete value and the array ydiscretord
DIMENSIONS
1: trait index , c 2: number of class (nmod(c))
listelev
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
listelev
DESCRIPTION
String value of a fixed effect
DIMENSIONS:
1: fixed effect index
NOTES
valueFixedEffect=listelev(ifix,valueIndex), 0 <= valueIndex <= nlev(ifix)
listModelTrait
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
listModelTrait
DESCRIPTION
Description of model for each trait
DIMENSIONS
1: trait index
NOTES
mapFileDefined
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
mapFileDefined
DESCRIPTION
flag to test if a user map file existe
mark
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
mark
DESCRIPTION
Name of the markers by chromosome
NOTES
marker(1,1) => name of first marker from the fisrt chromosome ch(1) ... Information from the map file (rec=1)
MAX_LINEAR_ITERATION
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
MAX_LINEAR_ITERATION
DESCRIPTION
Maximum iteration in the linear mode heteroscedastic to avoid infinity loop
NOTES
Information from the parameter file
mere
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
mere
DESCRIPTION
List of the dam name
modele
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
modele
DESCRIPTION
model for each fixed effects, each covariates and each interactions beetwen the QTL and the fixed effects.
DIMENSIONS
1: trait index
2: see notes
NOTES
modele (x,1) = number of fixed effets for the trait x
modele (x,2) = number of covariate for the trait x
modele (x,3) = number of qtl-fe for the trait x
modele (x,3+if) = value of fixed effect 'if' for the trait x
modele (x,3+nfix+icov) = value of covariate icov for the trait x
modele (x,3+nfix+ncov+ifix) = value of fixed effect with qtl effect for the trait x
size(model,2) = 3+2*nfix+ncov
Information from the trait file
nall
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nall
DESCRIPTION
Contains the number of allele by chromosome and marker
DIMENSIONS
1 : chromosome index 2 : marker index
namecov
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
namecov
DESCRIPTION
List of Covariate name
NOTES
Information from the model file
namefix
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
namefix
DESCRIPTION
List of fixed effects
NOTES
Information from the model file
namest
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
namest
DESCRIPTION
Number of female with estimability
DIMENSIONS
1: trait index
NOTES
if none dams are coupled with several sire, nmumest == namest
natureY
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
natureY
DESCRIPTION
Nature of each trait :
* 'r' for real or continue value
* 'i' for integer or discrete value
* 'c' for categorial value
Information from the model file
nb_value_pheno
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nb_value_pheno
DESCRIPTION
Contains the number of allele stored in the chromosome c
NOTES
QTLMap manage phenotype marker (allele) with integer id to improve performance
and minimize the memory space during a qtlmap process
SEE ALSO
m_qtlmap_data/value_pheno m_qtlmap_data/get_ind_pheno m_qtlmap_data/get_pheno
ncar
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
ncar
DESCRIPTION
Number of traits (continue and discrete)
ncarcat
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
ncarcat
DESCRIPTION
Number of categorials traits
nchr
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nchr
DESCRIPTION
Number of chromosome to analyse
NOTES
Information from the parameter file
ncov
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
ncov
DESCRIPTION
Number of covariate
NOTES
Information from the model file
nd
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nd
DESCRIPTION
Number of progenies : equivalent to size(animal)
ndelta
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
ndelta
DESCRIPTION
Contains the column "present trait" for each trait
DIMENSIONS
1: trait index 2: animal id referenced in animal
NOTES
size(2,presentc) == size(animal) Information from the trait file
ndm
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
ndm
DESCRIPTION
Id progeny by dam index
family of sire is building : One sire have severals dams who have severals progenies
EXAMPLE
do ip=1,np nm1=nmp(ip)+1 nm2=nmp(ip+1) do jm=nm1,nm2 nd1=ndm(jm)+1 nd2=ndm(jm+1) do id=nd1,nd2 ... end do end do end do
NDMIN
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
NDMIN
DESCRIPTION
Number of progenies to take in care estimable femal in the analysis
NOTES
Information from the parameter file
nfem
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nfem
DESCRIPTION
Number of female : equivalent to size(female)
NOTES
nfix
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nfix
DESCRIPTION
Number of fixed effects
NOTES
Information from the model file
ngm
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
ngm
DESCRIPTION
Number of grand dam : equivalent to size(gmere)
NOTES
Information from the genealogy file
ngmgp
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
ngmgp
DESCRIPTION
Grand dam id by grand sire index
EXAMPLE
do igp=1,ngp do jgm=ngmgp(igp)+1,ngmgp(igp+1) ... end do end do
NOTES
Information from the genealogy file
ngp
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
ngp
DESCRIPTION
Number of grand sire : equivalent to size(gpere)
nivx
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nivx
DESCRIPTION
Index value of fixed effect for each animal DIMENSIONS: 1: animal index 2: fixed effect index
NOTES
nivx(idAnimal,ifix)=valueIndex => value=listelev(ifix,valueIndex)
nlev
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nlev
DESCRIPTION
Number of levels per fixed effect DIMENSIONS: 1: fixed effect index
nm
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nm
DESCRIPTION
Number of dam : equivalent to size(mere)
NOTES
Information from the genealogy file
NMANQUE
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
NMANQUE
DESCRIPTION
Genotype code for missing value
NOTES
Information from the parameter file
nmes
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nmes
DESCRIPTION
Number of animal with phenotype marker
nmk
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nmk
DESCRIPTION
Number of the marker by chromosome
NOTES
nmk(1) => number of marker of the first chromosome ch(1) nmk(2) => number of marker of the second chromosome ... Information from the map file
nmod
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nmod
DESCRIPTION
Number of classes corresponding with discrete value
DIMENSIONS
1: trait index , c
nmp
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nmp
DESCRIPTION
id dam by sire index
family of sire is building : One sire have severals dams who have severals progenies
EXAMPLE
do ip=1,np nm1=nmp(ip)+1 nm2=nmp(ip+1) do jm=nm1,nm2 ... end do end do
nmumest
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nmumest
DESCRIPTION
Number of dam with estimability
DIMENSIONS
1: trait index
NOTES
np
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
np
DESCRIPTION
Number of sire : equivalent to size(pere)
NOTES
Information from the genealogy file
nrgm
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
nrgm
DESCRIPTION
Get reproductor id by grand dam index
EXAMPLE
do igp=1,ngp do jgm=ngmgp(igp)+1,ngmgp(igp+1) do kr=nrgm(jgm)+1,nrgm(jgm+1) ... end do end do end do
NOTES
Information from the genealogy file
numero
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
numero
DESCRIPTION
List of animal with phenotype marker information
NOTES
Information from the genotype file
opt_sib
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
opt_sib
DESCRIPTION
Treat family
NOTES
Information from argument of the execution
optim_H_PRECISION
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
optim_H_PRECISION
DESCRIPTION
Precision gradiant df/dx = f(x+h)-f(x-h)/2*h
SOURCE
1235 real(kind=dp) , public :: optim_H_PRECISION = 5.do-5
optim_maxeval
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
optim_maxeval
DESCRIPTION
number maximum of evaluation
SOURCE
1190 integer , public :: optim_maxeval = 0
optim_maxtime
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
optim_maxtime
DESCRIPTION
maxtime for each optimization
SOURCE
1199 real(kind=dp) , public :: optim_maxtime = 0
optim_tolf
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
optim_tolf
DESCRIPTION
tolerance for the function evaluation result f
SOURCE
1217 real(kind=dp) , public :: optim_tolf = 0
optim_tolg
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
optim_tolg
DESCRIPTION
tolerance for the gradient
SOURCE
1226 real(kind=dp) , public :: optim_tolg = 0
optim_tolx
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
optim_tolx
DESCRIPTION
tolerance for the variable x
SOURCE
1208 real(kind=dp) , public :: optim_tolx = 0
PAS
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
PAS
DESCRIPTION
Step analysis
NOTES
Information from the parameter file
pc_all
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
pc_all
DESCRIPTION
Frequencies alleles.
DIMENSIONS
1: chromosome index (ch) 2: marker index (m) 3: allele index ( 1 < allele index < nall(ch,m) )
pere
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
pere
DESCRIPTION
List of the sire name
pheno
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
pheno
DESCRIPTION
Phenotype marker (not oriented information) of each animal contains in array numero
DIMENSIONS
1 : chromosome index
2 : marker index
3 : animal index
4 : allele number (1 or 2)
NOTES
Information from the genotype file
PHPSEUIL
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
PHPSEUIL
DESCRIPTION
Minimal paternal phase probability
NOTES
The analysis is interrupted if for a sire, none of its phases reach this threshold Information from the parameter file
posi
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
posi
DESCRIPTION
Average position in Morgan by chromosome and marker
NOTES
posi(1,1) => position of the fisrt marker on the fisrt chromosome
...
Information from the map file (rec=3)
posif
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
posif
DESCRIPTION
Female position in Morgan by chromosome and marker
NOTES
posif(1,1) => position of the fisrt marker on the fisrt chromosome
...
Information from the map file (rec=5)
posim
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
posim
DESCRIPTION
Mal position in Morgan by chromosome and marker
NOTES
posim(1,1) => position of the fisrt marker on the fisrt chromosome
...
Information from the map file (rec=4)
presentc
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
presentc
DESCRIPTION
Array indicator to known if a trait is present for a progeny
DIMENSIONS
1: trait index 2: animal id referenced in animal
NOTES
size(2,presentc) == size(animal)
presentg
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
presentg
DESCRIPTION
Logical value for each progeny animal. True if the animal is genotyped on the chromosome CH
DIMENSIONS
1 : chromosome index 2 : animal index
NOTES
size (presentg) = size(animal) * nchr To known if a progeny is genotyped (from animal array) : animal(kd) => presentg(kd) , true if genotyped ; false otherwise
PROB_PHASE_DESC
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
PROB_PHASE_DESC
DESCRIPTION
Minimal probability to consider a predicted phase using flanking phased markers
NOTES
Information from the parameter file
PROB_SEUIL_RECOMB
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
PROB_SEUIL_RECOMB
DESCRIPTION
threshold of the test to identify an abnormal recombination rate
NOTES
prop
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
prop
DESCRIPTION
Proportion of the discrete classes
DIMENSIONS
1: trait index , c 2: number of class (nmod(c))
PRSEUIL
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
PRSEUIL
DESCRIPTION
Minimal maternal phase probability
NOTES
Threshold above which the probable maternal phases will be considered in the analysis Information from the parameter file
PSEUILHWE
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
PSEUILHWE
DESCRIPTION
Threshold to check the equilibrium of marker transmission within each family
NOTES
raceFileDefined
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
raceFileDefined
DESCRIPTION
flag to test if a user breed file existe
rep_reprom
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
rep_reprom
DESCRIPTION
List of the dam index among generation 1 of pedigree file (size(repro)=nr)
rep_reprop
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
rep_reprop
DESCRIPTION
List of the sire index among generation 1 of pedigree file (size(repro)=nr)
repfem
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
repfem
DESCRIPTION
Corresponding index between mere array and female array
NOTES
repfem(indmere)=indfemale => mere(indmere) == female(indfemale)
repmere
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
repmere
DESCRIPTION
Contains the reproductor index equivalent with an index dam
NOTES
repmere(inddam)=indrepro => mere(inddam) == repro(indrepro)
reppere
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
reppere
DESCRIPTION
Contains the reproductor index equivalent with an index sire
NOTES
reppere(indsire)=indrepro => pere(indsire) == repro(indrepro)
repro
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
repro
DESCRIPTION
List of reproductor name ( sire and dam )
NOTES
Information from the genealogy file
reprom
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
reprom
DESCRIPTION
List of dam name of animal of genealogy file ( offspring, sire and dam )
NOTES
Information from the genealogy file
reprop
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
reprop
DESCRIPTION
List of sire name of animal of genealogy file (offspring, sire and dam )
NOTES
Information from the genealogy file
rf
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
rf
DESCRIPTION
Xaldane distance computed with posif position
RhoG
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
RhoG
DESCRIPTION
Correlation genetic
DIMENSIONS
1 : Trait index 2 : Trait index
RhoP
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
RhoP
DESCRIPTION
Correlation phenotypique
DIMENSIONS
1 : Trait index 2 : Trait index
rm
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
rm
DESCRIPTION
Xaldane distance computed with posim position
seuil
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
seuil
DESCRIPTION
Thresholds on the underlying scale
DIMENSIONS
1: trait index , c 2: number of class (nmod(c))
SEUIL_CHO
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
SEUIL_CHO
DESCRIPTION
Cholesky threshold
NOTES
Information from the parameter file
sigt
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
sigt
DESCRIPTION
Standart deviation of each traits
DIMENSIONS
1: trait index
simTyp
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
simTyp
DESCRIPTION
flag to activate the simulation genotype
simulGenea
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
simulGenea
DESCRIPTION
flag to activate a simulation genealogy
simulMap
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
simulMap
DESCRIPTION
flag to activate a simulation map
simulTraits
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
simulTraits
DESCRIPTION
flag to activate a simulation trait
tabDevKey
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
tabDevKey
DESCRIPTION
array of values initialized from generic keys
THRES_CONFUSION
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
THRES_CONFUSION
DESCRIPTION
Threshold to test confusion betwwen level inside a contingence matrix
NOTES
Information from the parameter file
traitsFileDefined
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
traitsFileDefined
DESCRIPTION
flag to test if a user phenotypic file existe
value_pheno
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
value_pheno
DESCRIPTION
Contains the original string value of a phenotype marker by chromosome
NOTES
QTLMap manage phenotype marker (allele) with integer id to improve performance
and minimize the memory space during a qtlmap process
SEE ALSO
m_qtlmap_data/get_ind_pheno m_qtlmap_data/get_pheno
xmut
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
xmut
DESCRIPTION
Means of each traits
DIMENSIONS
1: trait index
y
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
y
DESCRIPTION
Value of discrete and continue value
DIMENSIONS
1: trait index 2: animal index
NOTES
Information from the trait file
ycategorial
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
ycategorial
DESCRIPTION
Value of categorial value
DIMENSIONS
1: trait index 2: animal index
NOTES
Information from the trait file
ydiscretord
[ Top ] [ m_qtlmap_data ] [ Variables ]
NAME
ydiscretord
DESCRIPTION
recodified class computed from discrete data
DIMENSIONS
1: trait index 2: animal index