| 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]])