m_qtlmap_haplotype_data
NAME
m_qtlmap_haplotype_data
SYNOPSIS
Storage of generating data by the haplotype package HAPLOTYPE
DESCRIPTION
Repository of haplotype data: - These data are instancied and initialized by the haplotype package - haplotype data are used by the analyse.
NOTES
SEE ALSO
DATA/m_qtlmap_data
comp_haplo_reduit
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
comp_haplo_reduit
DESCRIPTION
NOTES
count_haplo
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
count_haplo
DESCRIPTION
frequencies of the haplotypes found around a given location and having a length of longhap markers
DIMENSIONS
1 : number of positions tested on the chromosome
2 : haplotype index (as defined in num_haplo_pere, num_haplo_mere and num_haplo_desc)
NOTES
Generated by the HAPLOTYPE_LDLA package (Allocation and fill)
genotyp
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
genotyp
DESCRIPTION
Genotype (phenotype oriented) from individu referenced in the pheno array
DIMENSIONS
1 : chromosome index
2 : marker index
3 : animal index
4 : allele number (1 or 2)
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
genotypm
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
genotypm
DESCRIPTION
Within phase Genotype (phenotype oriented) of the dams referenced in the pheno array
DIMENSIONS
1 : chromosome index
2 : marker index
3 : animal x phase index
4 : allele number (1 or 2)
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
liste_haplo_reduit
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
liste_haplo_reduit
DESCRIPTION
NOTES
LONG_MIN_IBS
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
LONG_MIN_IBS
DESCRIPTION
NOTES
Initialized by m_qtlmap_parameter_file.f95
longhap
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
longhap
DESCRIPTION
Length of the haplotypes to be followed in LD analyses
NOTES
Information from the parameter file
name_haplo
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
name_haplo
DESCRIPTION
character name of the haplotype found around a given locationn and having a length of longhap markers
DIMENSIONS
1 : haplotype index (as defined in num_haplo_pere, num_haplo_mere and num_haplo_desc)
NOTES
Generated by the HAPLOTYPE_LDLA package (Allocation and fill)
name_haplo_complet
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
name_haplo_complet
DESCRIPTION
character name of possible fully known haplotype found around a given locationn and having a length of longhap markers
DIMENSIONS
1 : haplotype index (as defined in num_haplo_pere, num_haplo_mere and num_haplo_desc)
NOTES
Generated by the HAPLOTYPE_LDLA package (Allocation and fill)
name_haplo_reduit
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
name_haplo_reduit
DESCRIPTION
character name of the haplotype found around a given locationn and having a length of longhap markers
DIMENSIONS
1 : haplotype index (as defined in num_haplo_pere, num_haplo_mere and num_haplo_desc)
NOTES
Generated by the HAPLOTYPE_LDLA package (Allocation and fill)
nb_gam
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
nb_gam
DESCRIPTION
NOTES
nb_gam_desc
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
nb_gam_desc
DESCRIPTION
Number of possible different haplotypes carried by a progeny on a possibe maternal chromosome
DIMENSIONS
1 : progeny index
2 : possible haplotype id transmitted from the dam
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
nb_gam_mere
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
nb_gam_mere
DESCRIPTION
Number of possible different haplotypes carried by a dam x phase on a chromosome
DIMENSIONS
1 : dam genotype index
2 : allele number (1 /2)
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
nb_gam_pere
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
nb_gam_pere
DESCRIPTION
Number of possible different haplotypes carried by a sire on a chromosome
DIMENSIONS
1 : sire index
2 : allele number (1 /2)
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
nb_haplo
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
nb_haplo
DESCRIPTION
NOTES
nb_haplo_complet
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
nb_haplo_complet
DESCRIPTION
NOTES
NB_HAPLO_PRIOR
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
NB_HAPLO_PRIOR
DESCRIPTION
Number maximum of haplotype allowed
NOTES
Initialized by m_qtlmap_parameter_file.f95
nb_max_haplo
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
nb_max_haplo
DESCRIPTION
number of haplotypes found around tested location and having a length of longhap markers
ndesc
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
ndesc
DESCRIPTION
Get the progeny index from the index ngend
DIMENSIONS
1 : chromosome index
2 : index ngend
EXAMPLE
do ip=1,np ! for each sire nm1=nmp(ip)+1 nm2=nmp(ip+1) do jm=nm1,nm2 ! for each dam in the sire family ngeno1=ngenom(chr,jm)+1 ngeno2=ngenom(chr,jm+1) do ig=ngeno1,ngeno2 ! for each genotype possibly of the current dam nd1=ngend(chr,ig)+1 nd2=ngend(chr,ig+1) do kd=nd1,nd2 ! for each progeny associated with this genotype kkd=ndesc(chr,kd) ! Get the kkd index corresponding to the animal array if(presentc(ic,kkd)) then pp=-pdd(chr,kd,1,n)-pdd(chr,kd,2,n)+pdd(chr,kd,3,n)+pdd(chr,kd,4,n) pm=-pdd(chr,kd,1,n)+pdd(chr,kd,2,n)-pdd(chr,kd,3,n)+pdd(chr,kd,4,n) end if ... end do end do end do end do
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
ngend
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
ngend
DESCRIPTION
Progeny associated with a genotype dam in a sire family
DIMENSIONS
1 : chromosome index
2 : index genotype referenced in the ngenom array
EXAMPLE
do ip=1,np ! for each sire nm1=nmp(ip)+1 nm2=nmp(ip+1) do jm=nm1,nm2 ! for each dam in the sire family ngeno1=ngenom(chr,jm)+1 ngeno2=ngenom(chr,jm+1) do ig=ngeno1,ngeno2 ! for each genotype possibly of the current dam nd1=ngend(chr,ig)+1 nd2=ngend(chr,ig+1) do kd=nd1,nd2 ! for each progeny associated with this genotype ... end do end do end do end do
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
ngenom
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
ngenom
DESCRIPTION
DIMENSIONS
1 : chromosome index
2 : index dam
EXAMPLE
do ip=1,np nm1=nmp(ip)+1 nm2=nmp(ip+1) do jm=nm1,nm2 ngeno1=ngenom(c,jm)+1 ! first genotype of the dam jm ngeno2=ngenom(c,jm+1) ! last genotype of the dam jm do geno=ngeno1,ngeno2 ... end do end do end do
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
num_haplo_desc
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
num_haplo_desc
DESCRIPTION
Index of haplotype received by each progeny from its dam, defined by the central position and the length of this haplotype
DIMENSIONS
1 : progeny index
2 : allele number (1 to nb_gam)
3 : fully known haplotype
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
num_haplo_mere
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
num_haplo_mere
DESCRIPTION
Index of both halotype of dams, defined by the central position and the length of this haplotype
DIMENSIONS
1 : dam genotype index
2 : allele number (1 or 2)
3 : fully known haplotype
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
num_haplo_pere
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
num_haplo_pere
DESCRIPTION
Index of both halotype of sires, defined by the central position and the length of this haplotype
DIMENSIONS
1 : sire index
2 : allele number (1 or 2)
3 : fully known haplotype
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
pb_haplo_desc
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
pb_haplo_desc
DESCRIPTION
Probability of possible different haplotypes carried by a progeny on a possibe maternal chromosome
DIMENSIONS
1 : progenyindex
2 : fully known haplotype
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
pb_haplo_reduit
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
pb_haplo_reduit
DESCRIPTION
NOTES
pdd
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
pdd
DESCRIPTION
DIMENSIONS
1 : chromosome index (chr)
2 : index from ngend array
3 : Case of allele transmission 1 or 2 or 3 or 4 see above
4 : position index above the chromosome chr
NOTES
Generated by the HAPLOTYPE package (Allocation and fill) Cases of allele transmission ------------------------------------| | Dam | All1 | All2 | | Sire | | | |-----------------------------------| | All1 | 1 | 2 | |-----------|----------|------------| | All2 | 3 | 4 | |-------------------------------- --| pdd(ChIndex,progenyInd,1,POSITION) = probability of transmision All1 from Sire and All1 from Dam at the position POSITION pdd(ChIndex,progenyInd,2,POSITION) = probability of transmision All1 from Sire and All2 from Dam at the position POSITION pdd(ChIndex,progenyInd,3,POSITION) = probability of transmision All2 from Sire and All1 from Dam at the position POSITION pdd(ChIndex,progenyInd,4,POSITION) = probability of transmision All2 from Sire and All2 from Dam at the position POSITION 1 <= POSTION <= get_npo
SEE ALSO
m_qtlmap_data/get_ilong m_qtlmap_data/get_npo
phasm
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
phasp
DESCRIPTION
DIMENSIONS
1 : chromosome index
2 : index dam
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
phasp
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
phasp
DESCRIPTION
DIMENSIONS
1 : chromosome index
2 : index sire
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
prob_gam
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
prob_gam
DESCRIPTION
NOTES
prob_gam_mere
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
prob_gam_mere
DESCRIPTION
Probability of possible different haplotypes carried by a dam x phase on a chromosome
DIMENSIONS
1 : dam genotype index
2 : allele number (1 /2)
3 : fully known haplotype
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
prob_gam_pere
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
prob_gam_pere
DESCRIPTION
probability of possible different haplotypes carried by a sire on a chromosome
DIMENSIONS
1 : sire index
2 : allele number (1 /2)
3 : fully known haplotype
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
PROB_HAPLO_MIN
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
PROB_HAPLO_MIN
DESCRIPTION
miminum probability of a haplotype in the LD analysis
NOTES
Initialized by m_qtlmap_parameter_file.f95
prob_seuil_gam
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
prob_seuil_gam
DESCRIPTION
Minimal gamete probability (LDA Haplotype option)
probg
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
probg
DESCRIPTION
Probability of a dam genotype referenced in the ngend array
DIMENSIONS
1 : chromosome index
2 : index ngend
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
prot
[ Top ] [ m_qtlmap_haplotype_V2 ] [ Variables ]
NAME
prot
DESCRIPTION
buffer array for haplotypes modules
NOTES
lx,ndx,4
ptfin
[ Top ] [ m_qtlmap_haplotype_V2 ] [ Variables ]
NAME
ptfin
DESCRIPTION
buffer array for haplotypes modules
NOTES
dim : lx,ngdx,4
reconstructed
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
reconstructed
DESCRIPTION
is true when the marker phase is predicted
DIMENSIONS
1 : chromosome index
2 : animal index
3 : marker index
NOTES
Generated by the HAPLOTYPE package : m_qtlmap_phase_offspring (Allocation and fill)
shared_haplo
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
shared_haplo
DESCRIPTION
list of the maternally tranmitted segment wchich are IBS to one a the 2 sire haplotypes around a given position
DIMENSIONS
1 : animal index
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
tab_IBS
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
tab_IBS
DESCRIPTION
list of the gametes received by all progeny, assuming no double recombination between flanking informative markers
DIMENSIONS
1 : animal index 2 : marker index 3 : gamete number (1 or 2)
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)
tab_shared_haplo
[ Top ] [ m_qtlmap_haplotype_data ] [ Variables ]
NAME
tab_shared_haplo
DESCRIPTION
bilan of the maternally tranmitted segment which are IBS to one a the 2 sire haplotypes around a given position for each sire : nb of time the first ans second sire haplotypes are found, and frequency of discovery per length
DIMENSIONS
1 : sire ID
2 : sire haplotype (1 or 2)
3 : count ( total, then, per length
NOTES
Generated by the HAPLOTYPE package (Allocation and fill)