| rpt.IBD {KinMixLite} | R Documentation |
Replacing CPTs for selected mixture contributors with familial relationships
Description
Used after a call to DNAmixture with compile=FALSE,triangulate=FALSE, this function replaces the CPTs for the genotype allele count arrays for specified mixture contributors by those representing the specified relationship with each other and typed relatives
Usage
rpt.IBD(mixture, IBD="parent-child", typed.gts = NULL, inds = 1,
jtyped = ncol(IBD$patt)/2 - length(typed.gts) + seq_along(typed.gts),
jcontr = seq_along(inds),
targets=attr(IBD,'targets'), contribs=NULL, quiet=FALSE, all.freq = NULL, compile = TRUE)
rpt.typed.relatives(mixture, IBD="parent-child", typed.gts = NULL, inds = 1,
jtyped = ncol(IBD$patt)/2 - length(typed.gts) + seq_along(typed.gts),
jcontr = seq_along(inds),
targets=attr(IBD,'targets'), contribs=NULL, quiet=FALSE, all.freq = NULL, compile = TRUE)
rpt.typed.child(mixture, aca, ind=1)
replace.Ui.tables(mixture, aca, ind=1)
rpt.typed.parents(mixture, Mgt, Fgt, ind=1, compile=TRUE)
rpt.typed.relative(mixture, Rgt, IBD=c(0.25,0.5,0.25), ind=1, compile=TRUE)
Arguments
mixture |
DNAmixtures object created by previous call to |
IBD |
relationships between the specified individuals, as multi-person condensed coefficients of identity, in one of several representation; see Details. |
typed.gts |
list of 0 or more genotypes of relatives; the components of this list must
be named (with the id's of the relevant individuals) if |
inds |
vector of 1 or more integers: which ‘unknown’ contributors are we modelling by
amending their CPTs? The elements should be listed in the same order as the corresponding
pairs of columns of the IBD patterns in |
jtyped |
indices of pairs of columns of |
jcontr |
indices of pairs of columns of |
targets |
Character vector of the tags of the individuals referred to in |
contribs |
Character vector of the tags of the individuals included in the mixture, in order |
quiet |
should calculated values of inds, jtyped and jcontr be reported? |
all.freq |
alternative allele frequency database(s), see Details. |
compile |
logical flag: should mixture object be compiled on exit? |
ind |
as |
aca, Mgt, Fgt, Rgt |
individual genotypes, as allele count arrays |
Details
In using rpt.IBD or rpt.typed.relatives (which is identical), the correspondence between mixture contributors, specified relationships, and typed genotype profiles should be specified
either (preferably)
using targets, contribs and through the names of the components in typed.gts,
or (to be deprecated)
with inds, jcontr and jtyped:
the two representations should not be mixed up. If either targets or contribs specified, the former representation is assumed.
Special cases are treated slightly more efficiently:
rpt.typed.child: single contributor, single typed relative, parent or child;
rpt.typed.parents: single contributor, both parents typed;
rpt.typed.relative: single contributor, single typed relative.
Note that IBD$patt always has an even number of columns, two for each individual
in the joint relationship specified; jtyped and jcontr are vectors of
indices of these individuals, i.e. to pairs of adjacent columns of IBD$patt.
Multiple functions in this group can validly be called sequentially (with all but the
last having compile=FALSE) providing they reference different sets of
contributors among the targets, and that these sets are conditionally
independent given the typed genotypes specified.
There are multiple valid representations for relationships in the argument IBD –
as an IBD pattern distribution, via a pedigree, or. in the case of just two individuals.
via either a vector of 3 kappas or 9 Deltas (Jacquard's condensed coefficients of
identity). For full details, see convertIBD.
If IBD is missing, the default value represents parent-child.
In the interests of upward compatibility, in rpt.typed.child and
replace.Ui.tables (which are identical), the argument Cgt can be given as
either a genotype profile data frame, or an allele count array.
By default, the allele frequency database used for the founding genes is that
used when the mixture object is created, in an earlier call to DNAmixture.
A non-null value for the all.freq argument allows the
user to specify alternative database (s) for the founding genes. If its value
is an allele frequency database (in the format specified in
formats) then that database is used for all founding genes; if the
value of the argument is a list of such databases, then component k of the
list is used for allele frequencies for the founding gene labelled k in the
IBD argument. Note that this option allows modelling of mixtures where
different contributors are drawn from different populations, whether or not
there are relationships among individuals.
Value
Vector of marker-specific probabilities of the typed genotypes.
Author(s)
Peter Green (P.J.Green@bristol.ac.uk)
Examples
data(test2data)
data(NGMDyes)
## Fit 2-person mixture - baseline model
mixD<-DNAmixture(list(epg),k=2,C=list(0.001),database=db)
pars<-mixpar(rho=list(2),eta=list(100),xi=list(0.1),phi=list(c(U1=0.7,U2=0.3)))
baseline<-logL(mixD)(pars)
## Fit 2-person mixture model in which contributor 1 is parent of a typed individual Cgt
mixD<-DNAmixture(list(epg),k=2,C=list(0.001),database=db,triangulate=FALSE,compile=FALSE)
rpt.IBD(mixD,,list(Cgt))
log10LR<-(logL(mixD)(pars)-baseline)/log(10)
cat('log10 LR',log10LR,'\n')
## Fit 2-person mixture model in which contributor 1 is father of a typed individual Cgt
## with mother Mgt
mixD<-DNAmixture(list(epg),k=2,C=list(0.001),database=db,triangulate=FALSE,compile=FALSE)
rpt.IBD(mixD,,list(Mgt,Cgt))
log10LR<-(logL(mixD)(pars)-baseline)/log(10)
cat('log10 LR',log10LR,'\n')
## Fit 2-person mixture model in which contributors are two parents of a child with
## genotype Cgt, and a parent of one of them has genotype Rgt. Note the encoding of allele
## labels to reduce the complexity of the IBD pattern distribution IBD.
IBD<-list(patt=rbind(c(1,3,2,4,1,2,1,5),c(1,3,2,4,1,2,3,5)))
mixD<-DNAmixture(list(epg),k=2,C=list(0.001),database=db,triangulate=FALSE,compile=FALSE)
rpt.IBD(mixD,IBD,list(Cgt,Rgt),1:2)
log10LR<-(logL(mixD)(pars)-baseline)/log(10)
cat('log10 LR',log10LR,'\n')
## the same, with individuals and relationships denoted by character tags
mixD<-DNAmixture(list(epg),k=2,C=list(0.001),database=db,triangulate=FALSE,compile=FALSE)
rpt.IBD(mixD,IBD,list(c=Cgt,gf=Rgt),targets=c('f','m','c','gf'),contribs=c('f','m'))
log10LR<-(logL(mixD)(pars)-baseline)/log(10)
cat('log10 LR',log10LR,'\n')