qtlmt (version 0.1-1)

mtcmim: MTCMIM

Description

Multiple-trait composite multiple-interval mapping.

Usage

mtcmim(y, mpos, mdat, x, xid, dists, a, b, sigma, qtl=NULL,
   eps=NULL, win=Inf, range=0, pp=1, len=2, init=1,
   iter=2500,tol=1e-8)

Arguments

y

n by p matrix, whose columns are dependent variables.

mpos

data frame (id=marker index, ch=chromosome id, m=marker index on the chromosome, dist=genetic position in cM on the chromosome). Chromosome id should be an integer.

mdat

matrix of n rows; marker genotypes (1 or 0). Columns should correspond to markers in the order.

x

covariates; n by m numerical matrix.

xid

list of length p, xid[[j]] specifies columns of x as covariates for y[,j] .

dists

data frame (ch=chromosome id, mid=marker index, d=genetic position in cM on the chromosome); specifies initial QTL locations. Chromosome id should be an integer.

a

initial covariate effects including intercepts (if given).

b

initial QTL effects (if given).

sigma

initial residual variance-covariance (if given).

qtl

list of length p (if given); qtl[[j]] specifies qtls for y[,j], which are defined by rows of dists.

eps

data frame (y=which trait,q1=QTL one,q2=QTL two) (if not NULL); specifies epistatic terms.

win

window width of search around existing QTL. Ignored if range=0.

range

search range: genome-wide (0), the same chromosomes (-1).

pp

mapping population: BC-1, RIL-selfing-2, RIL-brother-sister-mating-3.

len

step length in search.

init

whether a, b and sigma are used as initial values.

iter

maximum number of iterations in a numerical process to estimate model parameters.

tol

convergence tolerance.

Value

• a list with the following components:
• loglik:
  log-likelihood of the final model
• a:
  covariate effects
• b:
  QTL effects
• sigma:
  residual variance-covariance
• qtl:
  QTL for each trait
• eps:
  epistatic terms
• dists:
  QTL locations

Examples

data(etrait)
qtl<- vector("list",16); qtl[[1]]<- c(1,2)
eps<- data.frame(y=1,q1=1,q2=2)
dists<- dists[c(4,11),]
x<- mdat - 3/2
o<- mtcmim(traits,mpos,mdat,x,xid,dists,
   qtl=qtl,eps=eps,win=5,range=-1,pp=2,len=1)