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MetaQtlData
into a
QtlPartition
and returns it.
MetaQtlAnalysis
analysis
for
a given value of the number of clusters k
and a
given trait name code
.
mrkIdxL
and mrkIdxR
.
object
to the layer.
cluster
this method
builds the consensus chromosome using a Weighted Least Square
strategy and returns the result as a MetaChrom
object.
MapCluster
framwork.ChromGraph
allows to link together
a Chromosome
and a QtlPartition
in order to be depicted into a graphic.Chromosome
objects into other kinds of objects or the inverse.mcidx[0..1][0..nmc-1]
.
a
and b
x
is an array of observed value and sd
an array of same
size than x
which stores the standard deviations of
the observed values.
data
performs the clustering
on each trait group and returns the results as an array of
MetaQtlResult
objects.
graph
context.
Qtl
into an object which class
implements the IBioLocus interface.
- func(double) -
Method in interface org.metaqtl.numrec.NumericalUtilities.Function
- Returns the value of the function in x.
- funcd(double) -
Method in interface org.metaqtl.numrec.NumericalUtilities.NRFunction
- Compute both the value and the derivate of the
function in x.
- function -
Variable in class org.metaqtl.bio.entity.bean.OntologyBean
- The function of the ontology.
criterion
this methods
looks into the array of EMResult
and find the model
which is optimal.
k
clusters.
Chromosomes
.
mrkIdxL < mrkIdxR
.
PrintStream
.
cidx
, the given trait name trait
and the given number of clusters k
.
getOptionValue(o,
null)
.
i
.
a
and b
MapCluster
.
g1
is
modified and will contain the result of the merge.
ChromCluster
.MetaChrom
which is
initialized by using the result
of the merge of the members of a ChromCluster
.
MetaMap
is a bundle of MetaChrom
objects.MetaMap
which will contain nchr
MetaChrom
objects.
MetaMap
objects into other kinds of objects or the inverse.MetaMap
.MetaQtlAnalysis
MetaQtlData
which
will represent the given array of Qtl
.
MetaQtlResult
is used to store the
results of a QTL meta analysis which has been performed
for a given trait group on a given chromosome.MultiFitResult
with the given number of observations N
and parameters M
.
Ontology
.Qtl
object into other kinds of objects or the inverse.QtlPartition
object.QtlProjAlgorithm
for
the given configuration of projection.
IBioLocus
objects.
x
is the
vector of observed values and sd
the
vector of their standard deviations.
maps
.
MetaQtlAnalysis
object.
Writer
to the algorithm
in order to write out the log info.
OutputStream
to the algorithm
in order to write out the log info.
A
is specified by the
matrix U
,V
and the vector w
as returned by the SVDecomposition() method.
A
, this routine computes its singular
value decomposition A = U.W.V' .
Chromosome
with the given cross design
and the given mapping context.
Chromosome
which represents
the chromosomes of the input mpe.
MetaMap
object into
an object which is consistent with the IBioGenome
interface.
IBioLocus interface
into a Qtl
.
- toString() -
Method in class org.metaqtl.bio.entity.LGroup
-
- toString() -
Method in class org.metaqtl.Chromosome
-
- toString() -
Method in class org.metaqtl.MultiFitResult
-
- totd -
Variable in class org.metaqtl.Chromosome
- The total distance of the chromosome.
- trait -
Variable in class org.metaqtl.MetaQtlResult
- The name of the trait.
- trait -
Variable in class org.metaqtl.Qtl
- The QTL trait data.
- traitNames -
Variable in class org.metaqtl.MetaQtlModel
- The trait names per chromosome.
- transformY(double) -
Method in class org.metaqtl.graph.ChromAxe
- Do a affine transformation of the given
position
d
which is assumed
to be in [0,dmax] in order to have its
representation in the chromosome axe.
- tree -
Variable in class org.metaqtl.MetaQtlResult
- The qtl tree
- tree -
Variable in class org.metaqtl.QtlPartition
- The Qtl tree.
- Tree - Class in org.metaqtl
- This class defines a tree.
- Tree() -
Constructor for class org.metaqtl.Tree
-
- Tree(TreeNode) -
Constructor for class org.metaqtl.Tree
-
- tree_method -
Variable in class org.metaqtl.algo.QtlTreeAlgorithm
- This global variable defines the method used by the aglomerative
hierarchical clustering.
- TREE_NODE_WIDTH -
Static variable in class org.metaqtl.graph.MetaGraphPar
-
- TreeFactory - Class in org.metaqtl.factory
- A factory to deal with distance trees.
- TreeFactory() -
Constructor for class org.metaqtl.factory.TreeFactory
-
- TreeNode - Class in org.metaqtl
- This class represents a node in a binary Tree obtained
when applying usual hirarchical clustering methods.
- TreeNode(int) -
Constructor for class org.metaqtl.TreeNode
- Creates a new instance of
TreeNode
with the given indice idx
.
- TreeNode(int, TreeNode[]) -
Constructor for class org.metaqtl.TreeNode
- Creates a new instance of
TreeNode
with the
given indice idx
and the children of the node.
- TreeNode() -
Constructor for class org.metaqtl.TreeNode
- Creates a new instance of
TreeNode
with
default attribute values.
- type -
Variable in class org.metaqtl.bio.entity.bean.LocusBean
-
- type -
Static variable in class org.metaqtl.bio.util.BioCrossTypes
-
- type -
Variable in class org.metaqtl.Qtl.QTLCross
- The type of the cross.
- TypesString -
Static variable in interface org.metaqtl.bio.IBioLocus
-
- typeToString(int) -
Static method in class org.metaqtl.bio.util.BioLocusTypes
-
stream
.
stream
the results
of a QTL meta-analysis.
analysis
on the given output stream stream
.
nodes
as an array of
TreeNode
on the given output stream stream.
nodes
as an array of
TreeNode
using the given writer writer.
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