getRelSignStrength {splicegear} | R Documentation |
Implementations of the SPLICE algorithm
getRelSignStrength(x, tissue = as.factor(1:ncol(x)), fun = mean, nipt = 30, nitt = 30, ...) getFinalRatio(x, tissue=as.factor(1:ncol(x)), fun=mean, ...)
x |
a matrix. One probe per line, one column per
sample. Typically this would be the slot exprs of an instance
of class ExprSet . |
tissue |
a covariate (factor) about the samples. |
fun |
a function to obtain a summary value (mean by default) |
nipt |
see reference. |
nitt |
see reference. |
... |
optional parameters for the function fun |
getFinalRatio
will call getRelSignStrength
. The
values are log-transformed. It is probably a good idea to avoid
feeding function with values that are already on log scale.
A matrix of the same dimension than the input x
, holding
'RSS' (Relative Signal Strength) or 'final ratios' respectively, as described in the reference. Two
attributes nip
and nit
are attached the returned matrix.
laurent@cbs.dtu.dk
Genome Research (2001), Hu et. al., vol. 11, p.1244
data(spliceset) ## The intensity values in the example are log-transformed. ## Undo by taking the exponential exprs(spliceset) <- exp(exprs(spliceset)) ## Re-order the rows of different slots to have the probes sorted by ## position spliceset <- sort.SpliceExprSet(spliceset) ## extract the expression matrix expr.m <- exprs(spliceset) fr <- getFinalRatio(expr.m, tissue=pData(spliceset@eset)[[1]])