loci               package:haplo.stats               R Documentation

_C_r_e_a_t_e _a _g_r_o_u_p _o_f _l_o_c_u_s _o_b_j_e_c_t_s _f_r_o_m _a _g_e_n_o_t_y_p_e _m_a_t_r_i_x, _a_s_s_i_g_n _t_o
'_m_o_d_e_l._m_a_t_r_i_x' _c_l_a_s_s.

_D_e_s_c_r_i_p_t_i_o_n:

     The function makes each pair of columns a locus object, which
     recodes alleles to numeric and saves the original alleles as an
     attribute of the model.matrix.

_U_s_a_g_e:

     loci(geno, locus.names, chrom.label=NULL, x.linked=FALSE, sex=NULL, 
          male.code="M", female.code="F", miss.val=NA, map=NA)

_A_r_g_u_m_e_n_t_s:

    geno: Matrix of alleles, such that each locus has a pair of
          adjacent columns of alleles, and the order of columns
          corresponds to the order of loci on a chromosome. If there
          are K loci, then ncol(geno) = 2*K. Rows represent alleles for
          each subject. 

locus.names : A vector containing the locus name for each locus. 

chrom.label : Chromosome Label  

x.linked : A logical value denoting whether the chromosome is X-linked. 

     sex: A vector containing the sex of each individual. If x.linked=F
          then argum ent sex is not required and may be left as the
          default value of NULL. 

male.code : The code denoting a male in the sex vector. 

female.code : The code denoting a female in the sex vector. 

miss.val : A vector of codes denoting missing values for the allele
          labels.   Note that NA will always be treated as a missing
          value, and alleles matching miss.val are assigned NA.  Also
          note that the original missing value code for a specific
          individual can not be retrieved  from the returned object. 

     map: An optional chromosome map of class "cmap" 

_V_a_l_u_e:

     An object of class "model.matrix", with all alleles recoded to a
     numeric value.  It contains the following attributes:

locus.names: A vector of labels for the loci, of length nloci. 

     map: Will be better defined later. 

x.linked: A logical value denoting whether the chromosome is X-linked. 

unique.alleles: The original allele labels are stored in the
          'unique.alleles' attribute. The ith item of the
          unique.alleles list is a vector of unique alleles for the ith
          locus. 

male.code: The code denoting a male in the sex vector. 

female.code: The code denoting a female in the sex vector. 

chrom.label: Chromosome Label 

_N_o_t_e:

     A matrix that contains all elements of mode character will be
     sorted in alphabetic order.

_S_e_e _A_l_s_o:

     locus, setupGeno

_E_x_a_m_p_l_e_s:

     # Create some loci to work with
     a1 <- 1:6
     a2 <- 7:12

     b1 <- c("A","A","B","C","E","D")
     b2 <-c("A","A","C","E","F","G")

     c1 <- c("101","10","115","132","21","112")
     c2 <- c("100","101","0","100","21","110")

     myloci <- data.frame(a1,a2,b1,b2,c1,c2)
     myloci <- loci(myloci, locus.names=c("A","B","C"),miss.val=c(0,NA))
     myloci

     attributes(myloci)

