ebam(x, cl, method = z.ebam, delta = 0.9, which.a0 = NULL, control = ebamControl(), gene.names = dimnames(x)[[1]], ...)
find.a0
,
i.e.\ an object of class FindA0
. Can also be a list (if method = chisq.ebam
or
method = trend.ebam
). For the latter case, see chisq.ebam
.
If x
is not a FindA0 object, then each row of x
(or
exprs(x)
, respectively) must correspond to a variable (e.g., a gene or a SNP), and each column to
a sample.x
is a FindA0
object.
Needs not to be specified if x
is a list.
Typically, cl
is specified by a vector of length ncol(x)
.
In the two class paired case, cl
can also
be a matrix with ncol(x)
rows and 2 columns. If x
is
an ExpressionSet object, cl
can also be a character string naming the column
of pData(x)
that contains the class labels of the samples.
In the one-class case, cl
should be a vector of 1's.
In the two class unpaired case, cl
should be a vector containing 0's
(specifying the samples of, e.g., the control group) and 1's (specifying,
e.g., the case group).
In the two class paired case, cl
can be either a numeric vector or a numeric matrix.
If it is a vector, then cl
has to consist of the integers between -1 and
$-n/2$ (e.g., before treatment group) and between 1 and $n/2$ (e.g.,
after treatment group), where $n$ is the length of cl
and $k$
is paired with $-k$, $k=1,\dots,n/2$. If cl
is a matrix, one
column should contain -1's and 1's specifying, e.g., the before and the after
treatment samples, respectively, and the other column should contain integer
between 1 and $n/2$ specifying the $n/2$ pairs of observations.
In the multiclass case and if method = chisq.ebam
or method = trend.ebam
,
cl
should be a vector containing integers between 1 and $g$, where $g$ is
the number of groups. In the two latter cases, cl
needs not to be specified, if
x
is a list. For details, see chisq.ebam
.
For examples of how cl
can be specified, see the manual of siggenes.method = z.ebam
,
a modified t- or F-statistic, respectively, will be computed as proposed by Efron et al. (2001).
If method = wilc.ebam
, a (standardized) Wilcoxon sum / signed rank statistic will
be used as expression score.
For an analysis of categorical data such as SNP data,
method
can be set to chisq.ebam
. In this case, Pearson's Chi-squared statistic
is computed for each row.
If the variables are ordinal and a trend test should be applied
(e.g., in the two-class case, the Cochran-Armitage trend test), method = trend.ebam
can be employed.
It is also possible to employ an user-written function for computing an user-specified
expression score. For details, see the vignette of siggenes.quan.a0
of find.a0
. If
NULL
, the suggested choice of find.a0
is used. Ignored if x
is a matrix, data
frame or ExpressionSet object.ebamControl
.nrow(x)
specifying the names of the variables. By default,
the row names of the matrix / data frame comprised by x
are used.method = z.ebam
, see
z.ebam
. If method = wilc.ebam
, see wilc.ebam
. If
method = chisq.ebam
, see chisq.ebam
.EBAM-class
, find.a0
, z.ebam
,
wilc.ebam
, chisq.ebam