haplo.score.w {GeneticsBase}R Documentation

Wrapper for computing score statistics to evaluate the association of a trait with haplotypes, when linkage phase is unknown and diploid marker phenotypes are observed among unrelated subjects

Description

wrapper for computing score statistics to evaluate the association of a trait with haplotypes, when linkage phase is unknown and diploid marker phenotypes are observed among unrelated subjects. For now, only autosomal loci are considered.

Usage

haplo.score.w(geneSetObj, 
              trait.type = "gaussian", 
              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())

Arguments

geneSetObj A geneSet object
trait.type Character string defining type of trait, with values of “gaussian”, “binomial”, “poisson”, “ordinal”.
offset Vector of offset when trait.type = “poisson”
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.
skip.haplo Skip score statistics for haplotypes with frequencies < skip.haplo. The default is for an expected count of 5 out of the 2*N haplotype occurrences.
locus.label Vector of labels for loci.
miss.val vector of values that represent missing alleles in geno.
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.
sim.control List of control parameters to determine how simulations are performed for simulated p-values. The list is created by the function score.sim.control and the default values of this function can be changed as desired. See score.sim.control for details.
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 haplo.em.control - see this function for more details

Details

Please refer to haplo.score for more details.

Value

List with the following components:

score.global Global statistic to test association of trait with haplotypes that have frequencies >= skip.haplo.
df Degrees of freedom for score.global.
score.global.p P-value of score.global based on chi-square distribution, with degrees of freedom equal to df.
score.global.p.sim P-value of score.global based on simulations (set equal to NA when simulate=F).
score.haplo Vector of score statistics for individual haplotypes that have frequencies >= skip.haplo.
score.haplo.p Vector of p-values for score.haplo, based on a chi-square distribution with 1 df.
score.haplo.p.sim Vector of p-values for score.haplo, based on simulations (set equal to NA when simulate=F).
score.max.p.sim Simulated p-value indicating for simulations the number of times a maximum score.haplo value exceeds the maximum score.haplo from the original data (equal to NA when simulate=F).
haplotype Matrix of hapoltypes analyzed. The ith row of haplotype corresponds to the ith item of score.haplo, score.haplo.p, and score.haplo.p.sim.
hap.prob Vector of haplotype probabilies, corresponding to the haplotypes in the matrix haplotype.
locus.label Vector of labels for loci, of length K (same as input argument).
simulate Same as function input parameter. If [T]rue, simulation results are included in the haplo.score object.
n.val.global Vector containing the number of valid simulations used in the global score statistic simulation. The number of valid simulations can be less than the number of simulations requested (by sim.control) if simulated data sets produce unstable variances of the score statistics.
n.val.haplo Vector containing the number of valid simulations used in the p-value simulations for maximum-score statistic and scores for the individual haplotypes.

Note

~~further notes~~

Author(s)

References

~put references to the literature/web site here ~

See Also

haplo.em.w, haplo.scan.w, haplo.score.slide.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.w"

[Package GeneticsBase version 1.2.0 Index]