haplo.score.slide.w {GeneticsBase}R Documentation

Wrapper for haplo.score.slide in haplo.stats package, which is used to identify sub-haplotypes from a group of loci

Description

Wrapper for haplo.score.slide, which is used to identify sub-haplotypes from a group of loci. Run haplo.score on all contiguous subsets of size n.slide from the loci in a genotype matrix (geno). From each call to haplo.score, report the global score statistic p-value. Can also report global and maximum score statistics simulated p-values.

Usage

haplo.score.slide.w(geneSetObj, 
                    trait.type = "gaussian", 
                    n.slide = 2, 
                    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”.
n.slide Number of loci in each contiguous subset. The first subset is the ordered loci numbered 1 to n.slide, the second subset is 2 through n.slide+1 and so on. If the total number of loci in geno is n.loci, then there are n.loci - n.slide + 1 total subsets.
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.slide for more details.

Value

List with the following components:

df Data frame with start locus, global p-value, simulated global p-value, and simulated maximum-score p-value.
n.loci Number of loci given in the genotype matrix.
simulate Same as parameter description above.
n.slide Same as parameter description above.
locus.label Same as parameter description above.
n.val.haplo Vector containing the number of valid simulations used in the maximum-score statistic p-value simulation. The number of valid simulations can be less than the number of simulations requested (by sim.control) if simulated data sets produce unstable variables of the score statistics.
n.val.global Vector containing the number of valid simulations used in the global score statistic p-value simulation.

Note

~~further notes~~

Author(s)

Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu

References

~put references to the literature/web site here ~

See Also

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

[Package GeneticsBase version 1.2.0 Index]