% --- Source file: snp.list.Rd ---
\name{snp.list}
\alias{snp.list}
\docType{data}
\title{
 List to describe the genotype data
}
\description{
 The list to describe the genotype data for \code{\link{snp.scan.logistic}}
}
\format{
      The format is: List of 7
       \describe{
           \item{file}{File to use. No default. }
           \item{file.type}{ 1-8 (see details). The default is 2.}
           \item{delimiter}{ The delimiter used in \code{file}. The default is "\\t" (a tab).}
           \item{in.miss}{Vector of values to denote the missing values in \code{file}.
                          The default is "  " (2 blank spaces). }
           \item{heter.codes}{ Vector of codes used for the heterozygous genotype.
                             If NULL, then it is assumed that the heterozygous genotype 
                             is of the form "AB", "Aa", "CT", ... etc, ie a 2-character
                             string with different characters (case sensitive).
                             The default is NULL.}
           \item{id.var}{   (Only for \code{file.type} = 3, 4, 6, 8) The subject id variable.
                             No default.}
           \item{sas.list}{  See \code{\link{sas.list}}. The default is NULL.}
       }
}


\details{ In this list, \code{file} must be specified. 
         If the SNPs are coded in the standard (0,1,2) coding, then
         set \code{heter.codes} to 1 (the heterozygous genotype).
          \cr \cr
                     \code{Types 1, 2, 5, 7} have data in the form: \cr \cr
                   \tabular{cccc}{
                       \tab subject1 \tab subject2 \tab subject3 \cr
                      snp1 \tab 0 \tab 2 \tab 1 \cr
                      snp2 \tab 1 \tab 1 \tab 0 
                    }
                    The first row
                    must contain the subject ids. Starting from row 2, the first
                    delimited field must contain the SNP id. The remaining
                    delimited fields contain the genotypes.
                    Rows are SNPs, columns are the subjects.
      \itemize{
          \item \code{Type 1} An .rda file created with the \code{save()} command. 
          \item \code{Type 2} A flat file that is in the form of the example above.
          \item \code{Type 5} A file compressed with WinZip.
          \item \code{Type 7} A file compressed with gzip.
      }
                    \code{Types 3, 4, 6, 8} have data of the form: \cr \cr
                    \tabular{ccc}{
                      id \tab snp1 \tab snp2  \cr
                      subject1 \tab 0 \tab 1 \cr
                      subject2 \tab 2 \tab 1 \cr
                      subject3 \tab 1 \tab 0 
                    }
                    There must also be a column containing the subject ids 
                    (see \code{id.var}) for these types.
      \itemize{
          \item \code{Type 3} A flat file that is in the form of the example above.
          \item \code{Type 4} A SAS data set (see \code{\link{sas.list}}).
          \item \code{Type 6} A file compressed with WinZip.
          \item \code{Type 8} A file compressed with gzip.
      }
}
\examples{
# Suppose the genotype data is a tab-delimited, type 2 file: c:/temp/data/geno1.txt.
#  Also assume the data has the trend coding 0, 1, 2 with NA as missing values.
# The below list is for processing the file.
\dontrun{
snp.list <- list(file="C:/temp/data/geno1.txt", delimiter="\t", file.type=2, 
                 heter.codes=1, in.miss=NA)
}
}
\keyword{misc}