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) used to compute the read count data. If not provided
all bins are assumed to have equal length.
n.bins.reduced
This 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) that will be
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