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]