Description Usage Arguments Details Value Author(s) References Examples

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").

1 | ```
createOffset(object, type, span = 1)
``` |

`object` |
a mixNBHMMDataSet |

`type` |
either 'sum' (sample-specific log sum of read counts), 'loess' (smoothed MA trend), or 'ratio' (median ratio). |

`span` |
proportion of data to be used in the smoothing (see details) |

If `type`

='sum', the offsets are calculated as the log column-wise sum of read counts + 1. If `type`

='loess',
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 `csaw`

. If `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).

1 2 |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.