Given a set of bioCond objects of which each has been
associated with a mean-variance curve, setPriorDfVarRatio assigns
a common number of prior degrees of freedom to all of them
and sets their variance ratio factors based on user-provided values.
There are few scenarios where you need to call this function
(see "Details").
setPriorDfVarRatio(
conds,
d0 = 0,
ratio.var = estimateVarRatio(conds),
.call = TRUE
)The argument list of
bioCond objects, with updated "df.prior" and
"ratio.var" components.
A list of bioCond objects, of which each has a
fit.info field describing its mean-variance curve (see also
fitMeanVarCurve).
A non-negative real specifying the number of prior degrees of freedom. Specifying a value other than 0 will lead to a warning (see also "Details").
A vector giving the variance ratio factors of the
bioConds. Elements are recycled if necessary. By default, it's
estimated by calling estimateVarRatio.
Never care about this argument.
Basically, the only reason for which you need to call this function is that
you don't want to borrow information between genomic intervals to improve
variance estimation. Therefore, this function should be in principle called
always with the default value (i.e., 0) for d0, in which case you
can still account for potential differences in global within-group
variability between groups of samples. Otherwise, you should empirically
estimate d0 via, for example, estimatePriorDf or
estimatePriorDfRobust.
There are two typical scenarios in which you don't want to borrow
information between genomic intervals. In the first one, the estimated
d0 derived by estimatePriorDfRobust is 0 because the
underlying variance structure is highly irregular. In the second one, there
are sufficient replicate samples (e.g., >7 profiles in each group) such that
observed variances alone could provide reliable variance estimates.
bioCond for creating a bioCond object;
fitMeanVarCurve for fitting a mean-variance curve and
using a fit.info field to characterize it;
estimatePriorDf and estimatePriorDfRobust
for estimating the number of prior degrees of freedom and adjusting
the variance ratio factors of a set of bioConds;
setPriorDf and setPriorDfRobust
for setting the number of prior degrees of freedom and accordingly
adjusting the variance ratio factors of a set of bioConds.