I am hoping to get a little more information about how to use DiffBind to deal with spike-in recalibration and the vignette is a little sparse on this topic. In section 7.6 there's the following code:
spikes <- dba.normalize(spikes, spikein = spikes.spikeins)
spikes.spikeins is loaded as part of
load(system.file('extra/spikes.rda',package='DiffBind'). The vignette states:
Note that precalculated background reads are included for the example in an object named spikes.spikeins, so we do not need to recount them for the vignette; we can pass the pre-calculated ones in instead. Normally, with access to thes pike-in reads, setting spikein=TRUE will result in the spike-in reads being counted.
I am wondering if we can get a little more code describing how spikes.spikeins was made --