Usage
select.reference.set(test.counts, reference.counts, bin.length = NULL,
n.bins.reduced = 0, data = NULL, formula = 'cbind(test, reference) ~ 1',
phi.bins = 1)
Arguments
test.counts
Read count data for the test sample (numeric, typically a vector of
integer values).
reference.counts
Matrix of read count data for a set of additional samples that can
be used as a comparison point for the test sample.
bin.length
Length (in bp) of each of the regions (often exons, but not
necessarily) that were used to compute the read count data
(i.e. what is provided in the argument test.counts of this
function).
If not provided all bins are assumed to have equa
n.bins.reduced
This optimization function can be slow when applied genome-wide. For
the purpose of building the reference sample, it is not necessary to
use the full data. The number provided by this argument specifies
the number of regions (typically exons
data
Defaults to NULL: A data frame of covariates that can be included in the
model.
formula
Defaults to 'cbind(test, reference) ~ 1'. This formula
will be used to fit the read count data. Covariates present in the
data frame (for example GC content) can be included in the right
hand side of the equation'. If covariates are provided t
phi.bins
Numeric integer (typically 1, 2, or 3) that specifies the number of windows
where the over-dispersion parameter phi can vary. It defaults to 1,
i.e. a single over-dispersion parameter, independently of read depth.