traitInfo: R6 Class representing information of traits (especially...
In KosukeHamazaki/myBreedSimulatR: R Breeding Simulator for K.Hamazaki
traitInfo R Documentation
R6 Class representing information of traits (especially simulated ones)
Description
traitInfo object store specific information of traits (especially simulated ones).
Public fields
lociInfo[lociInfo class] lociInfo of the specie
nMarkers[numeric] Number of markers for each chromosome
nTraits[numeric] Number of traits assumed in this breeding scheme
traitNames[character] Names of traits
nQTLs[matrix] Number of QTLs of each chromosome for each trait
qtlVarList[list] A list of variances of QTLs for additive/dominance, pleiotropy, and epistasis
$qtlPle: A variance of QTLs for pleiotropy
$qtlEach: A variance of QTLs for each trait (except epistasis)
$qtlEpi: A variance of QTLs for each trait (epistasis)
qtlOverlap[logical] If TRUE, pleiotropy across traits will be assumed
nOverlap[numeric] Number of QTLs common across traits for each chromosome
effCor[numeric] Correlation of pleiotropic QTL effects between traits
propDomi[numeric] Proportion of dominant effects for each trait
interactionMean[numeric] The expected number that each QTL interacts with others for each trait
actionTypeEpiSimple[logical] If TRUE, 'actionTypeEpi' will be same as
'actionType' for each QTL.
seedSelectMarker[numeric] Random seed for selecting marker information
seedSelectQTLEach[numeric] Random seed for selecting each QTL and its effect (it should have the same length as nTraits)
seedSelectQTLPle[numeric] Random seed for selecting pleiotropic QTLs and their effects
seedSelectQTLDom[numeric] Random seed for selecting QTL positions with dominant effects (it should have the same length as nTraits)
seedSelectQTLEpi[numeric] Random seed for selecting epistasis and its effect (it should have the same length as nTraits)
mrkPos[numeric] Marker positions
mrkPosEachChr[list] Marker positions for each chromosome
qtlPos[list] QTL positions for each trait
qtlEachPos[list] Positions of QTLs specific to one trait for each trait
qtlPlePos[list] Pleiotropic QTL positions for each trait
qtlEpiPos[list] Epistatic QTL positions for each trait
qtlPosEachChrList[list] QTL positions for each trait for each chromosome
qtlEachPosEachChrList[list] Positions of QTLs specific to one trait for each trait for each chromosome
qtlPlePosEachChrList[list] Pleiotropic QTL positions for each trait for each chromosome
qtlNamesList[list] QTL names for each trait
qtlEachNamesList[list] Names of QTLs common to one trait for each trait
qtlPleNamesList[list] Pleiotropic QTL names for each trait
qtlEpiNamesList[list] Epistatic QTL names for each trait
qtlAllNamesList[list] All QTL names for each trait (including epistatic effects)
actionType[list] A list of vectors representing additive by 0 and dominance by 1 for each trait
actionTypeEpi[list] A list of matrix representing additive by 0 and dominance by 1 for epitasis for each trait
qtlEff[list] QTL effects for each trait
qtlPleEff[list] Pleiotropic QTL effects for each trait
qtlEachEff[list] Effects of QTLs specific to one trait for each trait
qtlEpiEff[list] Epistatic QTL effects for each trait
qtlAllEff[list] All QTL effects for each trait (including epistasis)
nQTLsEach[numeric] Number of QTLs specific to each trait
nEpi[numeric] Number of epistatic effects
Methods
Public methods
Method new()
Create a new traitInfo object.
Usage
traitInfo$new(
lociInfo,
nMarkers,
nTraits = NULL,
traitNames = NULL,
nQTLs = NULL,
qtlVarList = NULL,
qtlOverlap = TRUE,
nOverlap = NULL,
effCor = NULL,
propDomi = NULL,
interactionMean = NULL,
actionTypeEpiSimple = TRUE,
qtlPleNamesList = NULL,
qtlEachNamesList = NULL,
seedSelectMarker = NA,
seedSelectQTLEach = NA,
seedSelectQTLPle = NA,
seedSelectQTLDom = NA,
seedSelectQTLEpi = NA
)
Arguments
lociInfo[lociInfo class] lociInfo of the specie
nMarkers[numeric] Number of markers for each chromosome
nTraits[numeric] Number of traits assumed in this breeding scheme
traitNames[character] Names of traits
nQTLs[matrix] Number of QTLs of each chromosome for each trait
qtlVarList[list] A list of variances of QTLs for additive/dominance, pleiotropy, and epistasis
$qtlPle: A variance of QTLs for pleiotropy
$qtlEach: A variance of QTLs for each trait (except epistasis)
$qtlEpi: A variance of QTLs for each trait (epistasis)
qtlOverlap[logical] If TRUE, pleiotropy across traits will be assumed
nOverlap[numeric] Number of QTLs common across traits for each chromosome
effCor[numeric] Correlation of pleiotropic QTL effects between traits
propDomi[numeric] Proportion of dominant effects for each trait
interactionMean[numeric] The expected number that each QTL interacts with others for each trait
actionTypeEpiSimple[logical] If TRUE, 'actionTypeEpi' will be same as
'actionType' for each QTL.
qtlPleNamesList[list] Pleiotropic QTL names for each trait
qtlEachNamesList[list] Names of QTLs common to one trait for each trait
seedSelectMarker[numeric] Random seed for selecting marker information
seedSelectQTLEach[numeric] Random seed for selecting each QTL and its effect (it should have the same length as nTraits)
seedSelectQTLPle[numeric] Random seed for selecting pleiotropic QTLs and their effects
seedSelectQTLDom[numeric] Random seed for selecting QTL positions with dominant effects (it should have the same length as nTraits)
seedSelectQTLEpi[numeric] Random seed for selecting epistasis and its effect (it should have the same length as nTraits)
Returns
A new 'traitInfo' object.
Examples
mySimInfo <- simInfo$new(simName = "Simulation Example",
simGeno = TRUE,
simPheno = TRUE,
nSimGeno = 1,
nSimPheno = 3,
nCoreMax = 4,
nCorePerGeno = 1,
nCorePerPheno = 3,
saveDataFileName = NULL)
### create specie information
mySpec <- specie$new(nChr = 3,
lChr = c(100, 150, 200),
specName = "Example 1",
ploidy = 2,
mutRate = 10^-8,
recombRate = 10^-7,
recombRateOneVal = FALSE,
chrNames = c("C1", "C2", "C3"),
nLoci = 100,
effPopSize = 100,
simInfo = mySimInfo,
verbose = TRUE)
### create SNP information
myLoci <- lociInfo$new(genoMap = NULL,
specie = mySpec,
seedSimGeno = NA,
lociNames = NULL,
founderNames = NULL)
### create traitInfo object
myTrait <- traitInfo$new(lociInfo = myLoci,
nMarkers = 80,
nTraits = 3,
nQTLs = c(4, 8, 3),
actionTypeEpiSimple = TRUE,
qtlOverlap = TRUE,
nOverlap = c(2, 3, 0),
effCor = 0.1,
propDomi = 0.2,
interactionMean = c(4, 1, 2))
print(myTrait)
Method genoMapDetail()
Detail information of map for marker genome
Usage
traitInfo$genoMapDetail(lociNames = NULL)
Arguments
lociNames[character] loci ids
Examples
myLoci$genoMapDetail()
myLoci$genoMapDetail("Loci_6")
Method print()
Display summary information about the object: traitInfo
Usage
traitInfo$print()
Method plot()
plot QTL map using the plotly package
Usage
traitInfo$plot(
alphaMarker = 0.05,
alphaQTL = 0.8,
sizeMarker = 5,
sizeQTLmin = 6,
sizeQTLmax = 12
)
Arguments
alphaMarker[numeric] transparency for markers see plot_ly
alphaQTL[numeric] transparency for QTLs see plot_ly
sizeMarker[numeric] size for markers
sizeQTLmin[numeric] size for QTL with minimum effect
sizeQTLmax[numeric] size for QTL with maximum effect
Examples
myLoci$plot(alphaMarker = 0.1, alphaQTL = 0.9,
sizeMarker = 5, sizeQTLmin = 6, sizeQTLmax = 12)
Method clone()
The objects of this class are cloneable with this method.
Usage
traitInfo$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
## ------------------------------------------------
## Method `traitInfo$new`
## ------------------------------------------------
mySimInfo <- simInfo$new(simName = "Simulation Example",
simGeno = TRUE,
simPheno = TRUE,
nSimGeno = 1,
nSimPheno = 3,
nCoreMax = 4,
nCorePerGeno = 1,
nCorePerPheno = 3,
saveDataFileName = NULL)
### create specie information
mySpec <- specie$new(nChr = 3,
lChr = c(100, 150, 200),
specName = "Example 1",
ploidy = 2,
mutRate = 10^-8,
recombRate = 10^-7,
recombRateOneVal = FALSE,
chrNames = c("C1", "C2", "C3"),
nLoci = 100,
effPopSize = 100,
simInfo = mySimInfo,
verbose = TRUE)
### create SNP information
myLoci <- lociInfo$new(genoMap = NULL,
specie = mySpec,
seedSimGeno = NA,
lociNames = NULL,
founderNames = NULL)
### create traitInfo object
myTrait <- traitInfo$new(lociInfo = myLoci,
nMarkers = 80,
nTraits = 3,
nQTLs = c(4, 8, 3),
actionTypeEpiSimple = TRUE,
qtlOverlap = TRUE,
nOverlap = c(2, 3, 0),
effCor = 0.1,
propDomi = 0.2,
interactionMean = c(4, 1, 2))
print(myTrait)
## ------------------------------------------------
## Method `traitInfo$genoMapDetail`
## ------------------------------------------------
myLoci$genoMapDetail()
myLoci$genoMapDetail("Loci_6")
## ------------------------------------------------
## Method `traitInfo$plot`
## ------------------------------------------------
myLoci$plot(alphaMarker = 0.1, alphaQTL = 0.9,
sizeMarker = 5, sizeQTLmin = 6, sizeQTLmax = 12)
KosukeHamazaki/myBreedSimulatR documentation built on Aug. 31, 2024, 3:55 p.m.
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| traitInfo | R Documentation |
R6 Class representing information of traits (especially simulated ones)
Description
traitInfo object store specific information of traits (especially simulated ones).
Public fields
lociInfo[lociInfo class] lociInfo of the specie
nMarkers[numeric] Number of markers for each chromosome
nTraits[numeric] Number of traits assumed in this breeding scheme
traitNames[character] Names of traits
nQTLs[matrix] Number of QTLs of each chromosome for each trait
qtlVarList[list] A list of variances of QTLs for additive/dominance, pleiotropy, and epistasis
$qtlPle: A variance of QTLs for pleiotropy$qtlEach: A variance of QTLs for each trait (except epistasis)$qtlEpi: A variance of QTLs for each trait (epistasis)
qtlOverlap[logical] If TRUE, pleiotropy across traits will be assumed
nOverlap[numeric] Number of QTLs common across traits for each chromosome
effCor[numeric] Correlation of pleiotropic QTL effects between traits
propDomi[numeric] Proportion of dominant effects for each trait
interactionMean[numeric] The expected number that each QTL interacts with others for each trait
actionTypeEpiSimple[logical] If TRUE, 'actionTypeEpi' will be same as 'actionType' for each QTL.
seedSelectMarker[numeric] Random seed for selecting marker information
seedSelectQTLEach[numeric] Random seed for selecting each QTL and its effect (it should have the same length as nTraits)
seedSelectQTLPle[numeric] Random seed for selecting pleiotropic QTLs and their effects
seedSelectQTLDom[numeric] Random seed for selecting QTL positions with dominant effects (it should have the same length as nTraits)
seedSelectQTLEpi[numeric] Random seed for selecting epistasis and its effect (it should have the same length as nTraits)
mrkPos[numeric] Marker positions
mrkPosEachChr[list] Marker positions for each chromosome
qtlPos[list] QTL positions for each trait
qtlEachPos[list] Positions of QTLs specific to one trait for each trait
qtlPlePos[list] Pleiotropic QTL positions for each trait
qtlEpiPos[list] Epistatic QTL positions for each trait
qtlPosEachChrList[list] QTL positions for each trait for each chromosome
qtlEachPosEachChrList[list] Positions of QTLs specific to one trait for each trait for each chromosome
qtlPlePosEachChrList[list] Pleiotropic QTL positions for each trait for each chromosome
qtlNamesList[list] QTL names for each trait
qtlEachNamesList[list] Names of QTLs common to one trait for each trait
qtlPleNamesList[list] Pleiotropic QTL names for each trait
qtlEpiNamesList[list] Epistatic QTL names for each trait
qtlAllNamesList[list] All QTL names for each trait (including epistatic effects)
actionType[list] A list of vectors representing additive by 0 and dominance by 1 for each trait
actionTypeEpi[list] A list of matrix representing additive by 0 and dominance by 1 for epitasis for each trait
qtlEff[list] QTL effects for each trait
qtlPleEff[list] Pleiotropic QTL effects for each trait
qtlEachEff[list] Effects of QTLs specific to one trait for each trait
qtlEpiEff[list] Epistatic QTL effects for each trait
qtlAllEff[list] All QTL effects for each trait (including epistasis)
nQTLsEach[numeric] Number of QTLs specific to each trait
nEpi[numeric] Number of epistatic effects
Methods
Public methods
Method new()
Create a new traitInfo object.
Usage
traitInfo$new( lociInfo, nMarkers, nTraits = NULL, traitNames = NULL, nQTLs = NULL, qtlVarList = NULL, qtlOverlap = TRUE, nOverlap = NULL, effCor = NULL, propDomi = NULL, interactionMean = NULL, actionTypeEpiSimple = TRUE, qtlPleNamesList = NULL, qtlEachNamesList = NULL, seedSelectMarker = NA, seedSelectQTLEach = NA, seedSelectQTLPle = NA, seedSelectQTLDom = NA, seedSelectQTLEpi = NA )
Arguments
lociInfo[lociInfo class] lociInfo of the specie
nMarkers[numeric] Number of markers for each chromosome
nTraits[numeric] Number of traits assumed in this breeding scheme
traitNames[character] Names of traits
nQTLs[matrix] Number of QTLs of each chromosome for each trait
qtlVarList[list] A list of variances of QTLs for additive/dominance, pleiotropy, and epistasis
$qtlPle: A variance of QTLs for pleiotropy$qtlEach: A variance of QTLs for each trait (except epistasis)$qtlEpi: A variance of QTLs for each trait (epistasis)
qtlOverlap[logical] If TRUE, pleiotropy across traits will be assumed
nOverlap[numeric] Number of QTLs common across traits for each chromosome
effCor[numeric] Correlation of pleiotropic QTL effects between traits
propDomi[numeric] Proportion of dominant effects for each trait
interactionMean[numeric] The expected number that each QTL interacts with others for each trait
actionTypeEpiSimple[logical] If TRUE, 'actionTypeEpi' will be same as 'actionType' for each QTL.
qtlPleNamesList[list] Pleiotropic QTL names for each trait
qtlEachNamesList[list] Names of QTLs common to one trait for each trait
seedSelectMarker[numeric] Random seed for selecting marker information
seedSelectQTLEach[numeric] Random seed for selecting each QTL and its effect (it should have the same length as nTraits)
seedSelectQTLPle[numeric] Random seed for selecting pleiotropic QTLs and their effects
seedSelectQTLDom[numeric] Random seed for selecting QTL positions with dominant effects (it should have the same length as nTraits)
seedSelectQTLEpi[numeric] Random seed for selecting epistasis and its effect (it should have the same length as nTraits)
Returns
A new 'traitInfo' object.
Examples
mySimInfo <- simInfo$new(simName = "Simulation Example",
simGeno = TRUE,
simPheno = TRUE,
nSimGeno = 1,
nSimPheno = 3,
nCoreMax = 4,
nCorePerGeno = 1,
nCorePerPheno = 3,
saveDataFileName = NULL)
### create specie information
mySpec <- specie$new(nChr = 3,
lChr = c(100, 150, 200),
specName = "Example 1",
ploidy = 2,
mutRate = 10^-8,
recombRate = 10^-7,
recombRateOneVal = FALSE,
chrNames = c("C1", "C2", "C3"),
nLoci = 100,
effPopSize = 100,
simInfo = mySimInfo,
verbose = TRUE)
### create SNP information
myLoci <- lociInfo$new(genoMap = NULL,
specie = mySpec,
seedSimGeno = NA,
lociNames = NULL,
founderNames = NULL)
### create traitInfo object
myTrait <- traitInfo$new(lociInfo = myLoci,
nMarkers = 80,
nTraits = 3,
nQTLs = c(4, 8, 3),
actionTypeEpiSimple = TRUE,
qtlOverlap = TRUE,
nOverlap = c(2, 3, 0),
effCor = 0.1,
propDomi = 0.2,
interactionMean = c(4, 1, 2))
print(myTrait)
Method genoMapDetail()
Detail information of map for marker genome
Usage
traitInfo$genoMapDetail(lociNames = NULL)
Arguments
lociNames[character] loci ids
Examples
myLoci$genoMapDetail()
myLoci$genoMapDetail("Loci_6")
Method print()
Display summary information about the object: traitInfo
Usage
traitInfo$print()
Method plot()
plot QTL map using the plotly package
Usage
traitInfo$plot( alphaMarker = 0.05, alphaQTL = 0.8, sizeMarker = 5, sizeQTLmin = 6, sizeQTLmax = 12 )
Arguments
alphaMarker[numeric] transparency for markers see plot_ly
alphaQTL[numeric] transparency for QTLs see plot_ly
sizeMarker[numeric] size for markers
sizeQTLmin[numeric] size for QTL with minimum effect
sizeQTLmax[numeric] size for QTL with maximum effect
Examples
myLoci$plot(alphaMarker = 0.1, alphaQTL = 0.9,
sizeMarker = 5, sizeQTLmin = 6, sizeQTLmax = 12)
Method clone()
The objects of this class are cloneable with this method.
Usage
traitInfo$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
## ------------------------------------------------
## Method `traitInfo$new`
## ------------------------------------------------
mySimInfo <- simInfo$new(simName = "Simulation Example",
simGeno = TRUE,
simPheno = TRUE,
nSimGeno = 1,
nSimPheno = 3,
nCoreMax = 4,
nCorePerGeno = 1,
nCorePerPheno = 3,
saveDataFileName = NULL)
### create specie information
mySpec <- specie$new(nChr = 3,
lChr = c(100, 150, 200),
specName = "Example 1",
ploidy = 2,
mutRate = 10^-8,
recombRate = 10^-7,
recombRateOneVal = FALSE,
chrNames = c("C1", "C2", "C3"),
nLoci = 100,
effPopSize = 100,
simInfo = mySimInfo,
verbose = TRUE)
### create SNP information
myLoci <- lociInfo$new(genoMap = NULL,
specie = mySpec,
seedSimGeno = NA,
lociNames = NULL,
founderNames = NULL)
### create traitInfo object
myTrait <- traitInfo$new(lociInfo = myLoci,
nMarkers = 80,
nTraits = 3,
nQTLs = c(4, 8, 3),
actionTypeEpiSimple = TRUE,
qtlOverlap = TRUE,
nOverlap = c(2, 3, 0),
effCor = 0.1,
propDomi = 0.2,
interactionMean = c(4, 1, 2))
print(myTrait)
## ------------------------------------------------
## Method `traitInfo$genoMapDetail`
## ------------------------------------------------
myLoci$genoMapDetail()
myLoci$genoMapDetail("Loci_6")
## ------------------------------------------------
## Method `traitInfo$plot`
## ------------------------------------------------
myLoci$plot(alphaMarker = 0.1, alphaQTL = 0.9,
sizeMarker = 5, sizeQTLmin = 6, sizeQTLmax = 12)
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