QTLMAP_TYPES
NAME
QTLMAP_TYPES -- Definition of qtlmap types.
SYNOPSIS
DESCRIPTION
NOTES
SEE ALSO
CORR_ALERT_TYPE
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NAME
CORR_ALERT_TYPE
DESCRIPTION
Description of a alert of a correlation to high between classical effect and a qtl effect
attributes members :
--------------------
qtl : number of qtl to test
ip : sire index where the correlation are finding
jm : dams index where the correlation are finding
corr : value of the correlation
ntlev : level of the qtl
name_effect : name of the classical effect
name_level : name of qtl level
NOTES
SOURCE
218 ! Type pour l impression des alerts de correlation trop eleve entre les effets polygenic, de nuisance et les effets qtls 219 type CORR_ALERT_TYPE 220 integer :: qtl=0 221 integer :: ip = -1 ! indice du pere sinon -1 222 integer :: jm = -1 ! indice de la mere concerne sinon -1 223 real(kind=dp) :: corr ! la correlation 224 integer :: ntlev =-1 ! le niveau du qtl concerne 225 character(len=LEN_W) :: name_effect ! le nom de l effet 226 character(len=LEN_W) :: name_level ! le nom du niveau 227 end type CORR_ALERT_TYPE
DESC_EFFECT_TYPE
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NAME
DESC_EFFECT_TYPE
DESCRIPTION
Description of an effect enumered in the INCIDENCE_TYPE attributes members : -------------------- name : name of the effect start : level start of the effect in the incidence matrix end : level end of the effect in the incidence matrix haveSubDesc : true if the effect have contains sub effect : sample :'Fixed effect A' is a effect that contains several level (value 1, value 2,...) listSubDesc : recursive structure that contains the sub effect
NOTES
This type is used by all analysis to make homogene the print of a estimation parameter solution
SOURCE
68 type DESC_EFFECT_TYPE 69 ! Name of effect 70 character(len=LEN_W) :: name 71 ! start ntniv 72 integer :: start = -1 73 ! end ntniv 74 integer :: end = -1 75 !If sub description : 76 logical :: haveSubDesc = .false. 77 ! sub effect name 78 type(DESC_EFFECT_TYPE),dimension(:),pointer :: listSubDesc => NULL() 79 ! true if the effect depends from the position in the linkage group 80 logical :: isVar = .false. 81 82 83 end type DESC_EFFECT_TYPE
GENEALOGY_TYPE
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NAME
GENEALOGY_TYPE
DESCRIPTION
NOTES
SOURCE
288 type GENEALOGY_TYPE 289 integer :: na = 0 ! number of animal (the population) 290 character(LEN=LEN_DEF) ,dimension(:) ,pointer :: listNA => null() ! the key ID => Name for each animal of the population 291 type(TRIO_TYPE) ,dimension(:) ,pointer :: trioKd => null() ! List of all trio parent link 292 integer ,dimension(:) ,pointer :: corranim => null() 293 294 integer ,dimension(:,:),pointer :: NCK ! nombre de descendant ayant une perf par KD pour le Caracteres i 295 integer ,dimension(:,:,:),pointer :: NCiCjK ! nombre de descendant ayant une perf par KD pour le Caracteres i et j 296 real(kind=dp) ,dimension(:,:,:),pointer :: corcd => null() 297 end type GENEALOGY_TYPE
model_trait
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NAME
DESC_EFFECT_TYPE
DESCRIPTION
NOTES
This type is used by all analysis to make homogene the print of a estimation parameter solution
SOURCE
31 type model_trait 32 ! number of fixed effect 33 integer :: nbfe 34 ! number of covariate 35 integer :: nbco 36 ! number of qtl with interaction 37 integer :: nbqtlinter 38 ! number of interaction with the qtl for each qtl with interaction defined 39 !size : nbqtlinter 40 integer ,dimension(:) ,pointer :: nbint => null() 41 ! size : nbfe : reference 42 integer ,dimension(:) ,pointer :: indexFixedEffect => null() 43 ! size : nbco : reference 44 integer ,dimension(:) ,pointer :: indexCovariate => null() 45 !size : nbqtlinter,nbint 46 integer ,dimension(:,:) ,pointer :: indexFixedEffectWithInteraction => null() 47 48 end type model_trait
TEST_NUISANCES_TYPE
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NAME
TEST_NUISANCES_TYPE
DESCRIPTION
Description of a nuisance test
attributes members :
--------------------
directeffect : false if the qtl are in interaction with the effect
name : name without the nuisance
df : freedom degree
lrt : likelihood ratio test
pvalue :
NOTES
SOURCE
244 !type pour l impression de test lin 245 type TEST_NUISANCES_TYPE 246 logical :: directeffect ! intra qtl (fixed effect) or direct effect 247 character(len=LEN_W) :: name ! name without the nuisances 248 integer :: df 249 real(kind=dp) :: lrt 250 real(kind=dp) :: pvalue 251 end type TEST_NUISANCES_TYPE
TRIO_TYPE
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NAME
TRIO_TYPE
DESCRIPTION
NOTES
SOURCE
270 type TRIO_TYPE 271 integer :: idSire = -1 ! sire 272 integer :: idDam = -1 ! dam 273 integer :: idKd = -1 ! Kd 274 real(kind=dp) ,dimension(MAXCAR) :: perfKd = 0.d0 275 logical ,dimension(MAXCAR) :: presentc =.false. 276 277 end type TRIO_TYPE
TYPE_INCIDENCE_SOLUTION
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NAME
TYPE_INCIDENCE_SOLUTION
DESCRIPTION
Description of a solution (estimation) of a analysis. All analysis fill this structure and give return the results.
attributes members :
--------------------
hypothesis : Test hypothesis of the analysis
sig : solution of the standart deviation of each sire
eqtl_print : logical array that referenced the effect to print in the context of a eqtl printing
eqtl solution are printing in a array, we give only the following information :
st.dev, mean, qtl effect. All estimation of fixed effect and covariate are skipped
groupeName : All effect are categorized : General Mean, Polygenic effect, Fixed effect, Covariate, Qtl Effect
nbParameterGroup : Number of parameter inside a group. sample, inside Polygenic effect : Sire A, Sire B,...
parameterName : Name of parameters by groupname
paramaterValue : Value of parameters by groupname
parameterVecsol : Estimability of parameters by groupname
parameterPrecis : Precision value of parameters by groupname
qtl_groupeName : Referenced the group of the QTL effect estimation
rhoi : residual correlation of traits
SOURCE
109 type TYPE_INCIDENCE_SOLUTION 110 ! Test based on the number of Qtls 111 integer :: hypothesis 112 ! formated to print 113 real (kind=dp) ,dimension(:,:),pointer :: sig => NULL() 114 ! Standart deviation for unknown haplotype dam 115 real (kind=dp) ,dimension(:,:),pointer :: unknown_dam_sig => NULL() 116 ! 117 logical ,dimension(:) ,pointer :: eqtl_print => NULL() 118 ! 119 character(len=LEN_W) ,dimension(:),pointer :: groupeName => NULL() 120 ! 121 integer ,dimension(:),pointer :: nbParameterGroup => NULL() 122 ! List of parameter name 123 character(len=LEN_W) ,dimension(:,:),pointer :: parameterName => NULL() 124 ! List of value 125 real (kind=dp) ,dimension(:,:),pointer :: paramaterValue => NULL() 126 127 logical , dimension(:,:) , pointer :: parameterVecsol => NULL() 128 129 real (kind=dp) ,dimension(:,:),pointer :: parameterPrecis => NULL() 130 131 ! Index postion in groupeName of qtl effect : ncar,nqtl 132 integer ,dimension(:,:),pointer :: qtl_groupeName => NULL() 133 134 real (kind=dp) ,dimension(:,:),pointer :: rhoi => NULL() 135 end type TYPE_INCIDENCE_SOLUTION
TYPE_LRT_SOLUTION
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NAME
TYPE_LRT_SOLUTION
DESCRIPTION
Description of the likelihood ratio test
attributes members :
--------------------
nqtl : hypothesis to test
lrtmax : maximum reached
dxmax : position where are the maximum
nxmax : position in the data structure where the maximum are reached
chrmax : chromosome where the maximum are reached
lrt1 : LRT curve under Hypothesis One (Only this hypothesis case)
pater_eff : paternal effect curve under Hypothesis One
mater_eff : maternal effect curve under Hypothesis One
xlrp : LRT sires surve under Hypothesis One
xlrm : LRT dams surve under Hypothesis One
lrt0_2 : LRT curve under Hypothesis Two against Zero (Only this hypothesis case)
lrt1_2 : LRT curve under Hypothesis Two against One (Only this hypothesis case)
pater_eff2 : paternal effect curve under Hypothesis Two
mater_eff2 : maternal effect curve under Hypothesis Two
xlrp2 : LRT sires surve under Hypothesis Two against One
xlrm2 : LRT dams surve under Hypothesis Two against One
NOTES
SOURCE
168 type TYPE_LRT_SOLUTION 169 ! Test based on the number of Qtls 170 integer :: nqtl = -1 171 ! LRT Maximum reached 172 real (kind=dp) ,dimension(:),pointer :: lrtmax => NULL() 173 ! Centimorgan positions of Qtls 174 !real (kind=dp) ,dimension(:),pointer :: dxmax => NULL() 175 ! Position of Qtl in data structure 176 integer ,dimension(:),pointer :: nxmax => NULL() 177 ! Chromosome where the position is localised 178 integer ,dimension(:),pointer :: chrmax => NULL() 179 !--------------------- QTL = 1 ----------------------------------- 180 ! chr,LRT curves if nqtl = 1 181 real (kind=dp) ,dimension(:,:),pointer :: lrt1 => NULL() 182 real (kind=dp) ,dimension(:,:,:),pointer :: pater_eff => NULL() 183 real (kind=dp) ,dimension(:,:,:),pointer :: mater_eff => NULL() 184 real (kind=dp) ,dimension(:,:,:),pointer :: xlrp => NULL() 185 real (kind=dp) ,dimension(:,:,:),pointer :: xlrm => NULL() 186 187 !--------------------- QTL = 2 --------------------------------- 188 ! chr,LRT curves if nqtl = 2 189 real (kind=dp) ,dimension(:,:,:,:),pointer :: lrt0_2 => NULL() 190 ! chr,LRT curves if nqtl = 2 191 real (kind=dp) ,dimension(:,:,:,:),pointer :: lrt1_2 => NULL() 192 ! chr1,chr2,np,npo1,npo2,2 (effet 1, effet2) 193 real (kind=dp) ,dimension(:,:,:,:,:,:),pointer :: pater_eff2 => NULL() 194 real (kind=dp) ,dimension(:,:,:,:,:,:),pointer :: mater_eff2 => NULL() 195 ! chr1,chr2,,np,npo1,npo2 196 real (kind=dp) ,dimension(:,:,:,:,:),pointer :: xlrp2 => NULL() 197 real (kind=dp) ,dimension(:,:,:,:,:),pointer :: xlrm2 => NULL() 198 end type TYPE_LRT_SOLUTION
MAXCAR
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NAME
MAXCAR
DESCRIPTION
max trait for TRIO_TYPE type description
NOTES