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.
haplo.scan.w(geneSetObj, width = 4, miss.val = c(0, NA), em.control = haplo.em.control(), sim.control = score.sim.control())
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. |
Please refer to haplo.scan
for more details.
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 |
~~further notes~~
Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu
~put references to the literature/web site here ~
haplo.em.w
, haplo.score.slide.w
, haplo.score.w
##---- 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"