\name{haplo.score.slide.w}
\alias{haplo.score.slide.w}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{Wrapper for haplo.score.slide in haplo.stats package, which is used to identify sub-haplotypes from a group of loci}
\description{
Wrapper for \code{\link[haplo.stats]{haplo.score.slide}}, which is used to identify sub-haplotypes from a group of loci.  Run
   haplo.score on all contiguous subsets of size n.slide from the
   loci in a genotype matrix (geno).  From each call to haplo.score,
   report the global score statistic p-value. Can also report global
   and maximum score statistics simulated p-values.
}
\usage{
haplo.score.slide.w(geneSetObj, 
                    trait.type = "gaussian", 
                    n.slide = 2, 
                    offset = NA, 
                    x.adj = NA, 
                    skip.haplo = 5/(2 * nrow(geno)), 
                    locus.label = NA, 
                    miss.val = c(0, NA), 
                    simulate = FALSE, 
                    sim.control = score.sim.control(), 
                    em.control = haplo.em.control())
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{geneSetObj}{ A geneSet object}
  \item{trait.type}{ Character string defining type of trait, with values of
   \dQuote{gaussian}, \dQuote{binomial}, \dQuote{poisson}, \dQuote{ordinal}.}
  \item{n.slide}{Number of loci in each contiguous subset.  The first subset
   is the ordered loci numbered 1 to n.slide, the second subset
   is 2 through \code{n.slide}+1 and so on.  If the total number of
   loci in geno is \code{n.loci}, then there are \code{n.loci} - \code{n.slide} + 1 total subsets.
}
  \item{offset}{ Vector of offset when trait.type = \dQuote{poisson}}
  \item{x.adj}{ Matrix of non-genetic covariates used to adjust the score
   statistics.  Note that intercept should not be included,  as
   it will be added in this function.
}
  \item{skip.haplo}{ Skip score statistics for haplotypes with frequencies <
   \code{skip.haplo}. The default is for an expected count of 5 out of
   the 2*N haplotype  occurrences.}
  \item{locus.label}{Vector of labels for loci.}
  \item{miss.val}{Vector of values that represent missing alleles in geno.}
  \item{simulate}{ Logical:  if [F]alse, no empirical p-values are computed; if
   [T]rue, simulations are performed. Specific simulation
   parameters can be controlled in the sim.control parameter
   list.
}
  \item{sim.control}{ list of control parameters to determine how simulations
   are performed for simulated p-values. The list is created by
   the function \code{\link[haplo.stats]{score.sim.control}} and the default values of this
   function can be changed as desired. See \code{\link[haplo.stats]{score.sim.control}} for
   details.}
  \item{em.control}{ A list of control parameters to determine how to perform
   the EM algorithm for estimating haplotype frequencies when
   phase is   unknown. The list is created by the function
   \code{\link[haplo.stats]{haplo.em.control}} - see this function for more details}
}
\details{
Please refer to \code{\link[haplo.stats]{haplo.score.slide}} for more details.
}
\value{
List with the following components:

\item{df}{
Data frame with start locus, global p-value, simulated global p-value,
and simulated maximum-score p-value.
}
\item{n.loci}{
Number of loci given in the genotype matrix.
}
\item{simulate}{
Same as parameter description above.
}
\item{n.slide}{
Same as parameter description above.
}
\item{locus.label}{
Same as parameter description above.
}
\item{n.val.haplo}{
Vector containing the number of valid simulations used in the
maximum-score statistic p-value simulation.  The number of valid simulations
can be less than the number of simulations requested (by sim.control)
if simulated data sets produce unstable variables of the score
statistics. 
}
\item{n.val.global}{
Vector containing the number of valid simulations used in the
global score statistic p-value simulation.  
}
}
\references{ ~put references to the literature/web site here ~ }
\author{ Weiliang Qiu \email{stwxq@channing.harvard.edu}, Ross Lazarus \email{ross.lazarus@channing.harvard.edu}}
\note{ ~~further notes~~ 
}
\seealso{ \code{\link{haplo.em.w}}, \code{\link{haplo.scan.w}}, \code{\link{haplo.score.w}}}
\examples{
##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
"haplo.score.slide.w"
}
\keyword{ misc }% at least one, from doc/KEYWORDS