Should not be called directly, but via ebam(..., method = fuzzy.ebam) or sam(..., method = fuzzy.stat), respectively.
fuzzy.ebam(data, cl, type = c("asymptotic", "permutation", "abf"), W = NULL, logbase = exp(1), addOne = TRUE, df.ratio = NULL, n.interval = NULL, df.dens = 5, knots.mode = TRUE, type.nclass = c("FD", "wand", "scott"), fast = FALSE, B = 100, B.more = 0.1, B.max = 30000, n.subset = 10, rand = NA)
fuzzy.stat(data, cl, type = c("asymptotic", "permutation", "abf"), W = NULL, logbase = exp(1), addOne = TRUE, B = 100, B.more = 0.1, B.max = 30000, n.subset = 10, rand = NA)getMatFuzzy based on the confidences for the three possible genotypes computed
by preprocessing algorithms such as CRLMM.
data contains the fuzzy genotype calls for the
cases (1) and which the controls (0). Thus, the length of cl must be equal to the number of columns of data.
"asymptotic", the trend statistic of Louis et al. (2010)
is used directly, and EBAM or SAM are performed assuming that under the null hypothesis this test statistic follows am asymptotic
standard normal distribution. If "permutation", a permutation procedure is employed to estimate the null distribution of this
test statistic. If "abf", Approximate Bayes Factors (ABF) proposed by Wakefield (2007) are determined from the trend statistic,
and EBAM or SAM are performed on these ABFs or transformations of these ABFs (see in particular logbase and addOne). In
the latter case, again, a permutation procedure is used in EBAM and SAM to, e.g., compute posterior probabilities of association.
nrow(data) consisting of
positive values. Ignored if type = "asymptotic" or type = "permutation". For details, see
abf.
type = "abf", then the ABFs are not directly used in the analysis, but a
log-transformation (with base logbase) of the ABFs. If the ABFs should not be transformed, logbase can be set to NA.
Ignored if type = "asymptotic" or type = "permutation".
TRUE, log(ABF + 1, base=logbase) is used as
test score in EBAM or SAM. If FALSE, log(ABF, base = logbase) is considered. Only taken into account when
type = "abf" and logbase is not NA.
type = "asymptotic". If not specified, df.ratio is set to 3 if type = "abf",
and to 5 if type = "permutation"
type = "permutation" or type = "abf"), or in the Poisson regression used to estimate
the density of the observed $z$-values (if type = "asymptotic").
If NULL, n.interval is estimated by the method specified by type.nclass, where at least 139 intervals
are considered if type = "permutation" or type = "abf".
ebam with type = "asymptotic". Otherwise, ignored.
df.dens - 1 knots are centered around the
mode and not the median of the density when fitting the Poisson regression model to estimate
the density of the observed $z$-values in an application of ebam with type = "asymptotic"
(for details on this density estimation, see denspr). Ignored if type = "permutation"
or type = "abf".
type = "permutation", type = "abf", or
n.interval is specified. Can be either "FD" (default), "wand", or "FD".
For details, see denspr.
FALSE the exact number of permuted test scores that are
more extreme than a particular observed test score is computed for each of
the variables/SNPs. If TRUE, a crude estimate of this number is used.
type = "asymptotic".
B.more)*B, full permutation will be done.
Otherwise, B permutations are used.
B.max, B randomly selected permutations will be used
in the computation of the null distribution. Otherwise, B random draws
of the group labels are used.
B
permutations are divided when computing the permuted $z$-values. Please note
that the meaning of n.subset differs between the SAM and the EBAM functions.
NA, the random number generator
will be set into a reproducible state.
ebam or sam.Tusher, V.G., Tibshirani, R., and Chu, G. (2001). Significance Analysis of Microarrays Applied to the Ionizing Radiation Response. PNAS, 98, 5116-5121. Wakefield, J. (2007). A Bayesian Measure of Probability of False Discovery in Genetic Epidemiology Studies. AJHG, 81, 208-227.
ebam, sam, EBAM-class, SAM-class