haplo.scan.w {GeneticsBase}R Documentation

Wrapper for searching for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window

Description

Wrapper for searching for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window.

Usage

haplo.scan.w(geneSetObj, 
             width = 4, 
             miss.val = c(0, NA), 
             em.control = haplo.em.control(), 
             sim.control = score.sim.control())

Arguments

geneSetObj A geneSet object
width Width of sliding the window
miss.val Vector of values that represent missing alleles in geno.
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.
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.

Details

Please refer to haplo.scan for more details.

Value

A list that has class haplo.scan, which contains the following items:

call The call to haplo.scan.w
scan.df A data frame containing the maximum test statistic for each window around each locus, and its simulated p-value.
max.loc The loci (locus) which contain(s) the maximum observed test statistic over all haplotype lengths and all windows.
globalp A p-value for the significance of the global maximum statistic.
nsim Number of simulations performed

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.score.slide.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.scan.w"

[Package GeneticsBase version 1.8.0 Index]