haplo.stats (version 1.7.6)

haplo.group: Frequencies for Haplotypes by Grouping Variable

Description

Calculate maximum likelihood estimates of haplotype probabilities for the entire dataset and separately for each subset defined by the levels of a group variable. Only autosomal loci are considered.

Usage

haplo.group(group, geno, locus.label=NA, 
            miss.val=0, weight=NULL, 
            control=haplo.em.control())

Arguments

group

Group can be of logical, numeric, character, or factor class type.

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 geno has 2*K columns. Rows represent all observed alleles for each sub

locus.label

Vector of labels for loci, of length K (see definition of geno matrix).

miss.val

Vector of codes for allele missing values.

weight

weights for observations (rows of geno matrix). One reason to use is to adjust for disproportionate sample of sub-groups. Weights only used in the frequency calculation for the pooled subject.

control

list of control parameters for haplo.em (see haplo.em.control).

Value

• A list as an object of the haplo.group class. The three elements of the list are described below.
• group.df
  A data frame with the columns described as follows. -haplotype: Names for the K columns for the K alleles in the haplotypes. -total: Estimated frequencies for haplotypes from the total sample. -group.name.i: Estimated haplotype frequencies for the haplotype if it occurs in the group referenced by 'i'. Frequency is NA if it doesn't occur for the group. The column name is the actual variable name joined with the ith level of that variable.
• group.count
  Vector containing the number of subjects for each level of the grouping variable.
• n.loci
  Number of loci occuring in the geno matrix.

References

Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. "Score tests for association of traits with haplotypes when linkage phase is ambiguous." Amer J Hum Genet. 70 (2002): 425-434.

Details

Haplo.em is used to compute the maximum likelihood estimates of the haplotype frequencies for the total sample, then for each of the groups separately.

See Also

print.haplo.group, haplo.em

Examples

data(hla.demo)
  geno <- as.matrix(hla.demo[,c(17,18,21:24)])

# remove any subjects with missing alleles for faster examples, 
# but you may keep them in practice
  keep <- !apply(is.na(geno) | geno==0, 1, any)
  hla.demo <- hla.demo[keep,]
  geno <- geno[keep,]
  attach(hla.demo)
  
  y.ord <- as.numeric(resp.cat)
  y.bin <-ifelse(y.ord==1,1,0)
  group.bin <- haplo.group(y.bin, geno, miss.val=0)
  print.haplo.group(group.bin)