Given a mixNBHMMDataSet, this function creates offsets for peak calling. The current implementation can output three different sets of offsets: the sample-specific log sum of read counts (type="sum"), smoothed MA trend (type="loess"), or median ratio (type="ratio").
either 'sum' (sample-specific log sum of read counts), 'loess' (smoothed MA trend), or 'ratio' (median ratio).
proportion of data to be used in the smoothing (see details)
type='sum', the offsets are calculated as the log column-wise sum of read counts + 1. If
the offsets will be the smoothed curve fitted on the MA plot that compares each sample's read counts + 1 over the geometric mean across all samples.
The smoothing approach has been similarly implemented in
type='ratio', the offsets will be the median ratio of the sample's
read counts + 1 over the geometric mean across all samples.
The mixNBHMMDataSet with an 'offset' assay filled in.
Pedro L. Baldoni, [email protected]
https://github.com/plbaldoni/mixNBHMM Nucleic Acids Research 44, e45 (2015).
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