Usage
seqhap(y, geno, pos, locus.label=NA, weight=NULL,
mh.threshold=3.84, r2.threshold=0.95, haplo.freq.min=0.005,
miss.val=c(0, NA), sim.control=score.sim.control(),
control=haplo.em.control())
## S3 method for class 'seqhap':
print(x, digits=max(options()$digits-2, 5), ...)Arguments
y
vector of binary response (1=case, 0=control). The length is equal
to the number of rows in geno.
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 the alleles for each subject. Currently,
pos
vector of physical positions (or relative physical positions) for
loci. If there are K loci, length(pos)=K. The scale (in kb, bp, or
etc.) doesn't affect the results.
locus.label
vector of labels for the set of loci
weight
weights for observations (rows of geno matrix).
mh.threshold
threshold for the Mantel-Haenszel statistic that evaluates whether a
locus contributes additional information of haplotype association to
disease, conditional on current haplotypes. The default is 3.84, which
is the 95th percentile of the chi-square distr
r2.threshold
threshold for a locus to be skipped. When scanning locus k, loci
with correlations r-squared (the square of the Pearson's correlation)
greater than r2.threshold with locus k will be ignored, so that the haplotype
growing process continues for markers that
haplo.freq.min
the minimum haplotype frequency for a haplotype to be included in the
association tests. The haplotype frequency is based on the EM
algorithm that estimates haplotype frequencies independent of trait.
miss.val
vector of values that represent missing alleles.
sim.control
A list of control parameters to determine how simulations are
performed for permutation p-values, similar to the strategy in
haplo.score. The list is created by the function
score.sim.control and the default values of this function can be
changed as des
control
A list of parameters that control the EM algorithm for estimating
haplotype frequencies when phase is unknown. The list is created by
the function haplo.em.control - see this function for more details.
x
a seqhap object to print
digits
Number of significant digits to print for numeric values
...
Additional parameters for the print method