haplo.score.slide.w {GeneticsBase} | R Documentation |
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.
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())
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 |
Please refer to haplo.score.slide
for more details.
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. |
~~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.scan.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.score.slide.w"