cat.ebam {siggenes} | R Documentation |
Generates the required statistics for an Empirical Bayes Analysis of Microarrays (EBAM) of categorical data such as SNP data.
Should not be called directly, but via ebam(..., method = cat.ebam).
cat.ebam(data, cl, approx = FALSE, B = 100, n.split = 1, check.for.NN = FALSE, lev = NULL, B.more = 0.1, B.max = 50000, n.subset = 10, fast = FALSE, n.interval = NULL, df.ratio = 3, df.dens = NULL, knots.mode = NULL, type.nclass = "wand", rand = NA)
data |
a matrix or data frame. Each row must correspond to a variable/SNP, and each column to a sample |
cl |
a numeric vector of length ncol(data) indicating to which class
a sample belongs. Must consist of the
integers between 1 and c, where c is the number of different groups |
approx |
should the null distribution be approximated by a Chisquare-distribution? |
B |
the number of permutations used in the estimation of the null distribution, and hence, in the computation of the expected z-values. |
n.split |
number of chunks in which the variables are splitted in the computation
of the values of the test statistic. Currently, only available if approx = TRUE .
By default, the test scores of all variables are calculated simultaneously.
If the number of variables or observations is large, setting n.split to a
larger value than 1 can help to avoid memory problems |
check.for.NN |
if TRUE , it will be checked if any of the genotypes
is equal to "NN". Can be very time-consuming when the data set is high-dimensional |
lev |
numeric or character vector specifying the codings of the levels of the variables/SNPs. Must only be specified if the variables are not coded by the integers between 1 and the number of levels. Can also be a list. In this case, each element of this list must be a numeric or character vector specifying the codings, where all elements must have the same length |
B.more |
a numeric value. If the number of all possible permutations is smaller
than or equal to (1+B.more )*B , full permutation will be done.
Otherwise, B permutations are used |
B.max |
a numeric value. If the number of all possible permutations is smaller
than or equal to 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 |
n.subset |
a numeric value indicating in how many subsets the 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 |
fast |
if 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 |
n.interval |
the number of intervals used in the logistic regression with
repeated observations for estimating the ratio f0/f
(if approx = FALSE ), or in the Poisson regression used to estimate
the density of the observed z-values (if approx = TRUE ).
If NULL , n.interval is set to 139 if approx = FALSE ,
and estimated by the method specified by type.nclass if approx = TRUE |
df.ratio |
integer specifying the degrees of freedom of the natural cubic
spline used in the logistic regression with repeated observations. Ignored
if approx = TRUE |
df.dens |
integer specifying the degrees of freedom of the natural cubic
spline used in the Poisson regression to estimate the density of the observed
z-values. Ignored if approx = FALSE .
If NULL , df.dens is set to 3 if the degrees of freedom
of the appromimated null distribution, i.e. the ChiSquare-distribution,
are less than or equal to 2, and otherwise df.dens is set to 5 |
knots.mode |
if TRUE the df.dens - 1 knots are centered around the
mode and not the median of the density when fitting the Poisson regression model.
Ignored if approx = FALSE .
If not specified, knots.mode is set to
TRUE if the degrees of freedom of the approximated null distribution, i.e.
tht ChiSquare-distribution, are larger than or equal to 3, and otherwise
knots.mode is set to FALSE . For details on this density estimation,
see denspr |
type.nclass |
character string specifying the procedure used to compute the
number of cells of the histogram. Ignored if approx = FALSE or
n.interval is specified. Can be either
"wand" (default), "scott" , or "FD" . For details, see
denspr |
rand |
numeric value. If specified, i.e. not NA , the random number generator
will be set into a reproducible state |
For each variable, Pearson's Chi-Square statistic is computed to test if the distribution of the variable differs between several groups. Since only one null distribution is estimated for all variables as proposed in the original EBAM application of Efron et al. (2001), all variables must have the same number of levels/categories.
a list containing statistics required by ebam
This procedure will only work correctly if all SNPs/variables have the same number of levels/categories.
Holger Schwender, holger.schw@gmx.de
Efron, B., Tibshirani, R., Storey, J.D. and Tusher, V. (2001). Empirical Bayes Analysis of a Microarray Experiment, JASA, 96, 1151-1160.
Schwender, H. (2007). Empirical Bayes Analysis of Single Nucleotide Polymorphisms. Technical Report, Department of Statistics, University of Dortmund. To appear soon.
Schwender, H., Krause, A. and Ickstadt, K. (2003). Comparison of the Empirical Bayes and the Significance Analysis of Microarrays. Technical Report, SFB 475, University of Dortmund, Germany.