normalize_timecourse

The integration site readouts to adjust.

readouts

A matrix with columns "IS" and "Clone" that assigns each
integration site to a clone.

Whether the clones should be put in the first rows of the
resulting time course.

rec_first

Whether to represent the integration sites by their
respective clone.

reduce_clones

Each integration site is replaced by its clone. The size of the clone is
adjusted to be the mean size of the integration sites within it. For
integration sites that are not mentioned in `rec`, we adjust by the average
number of integration sites per clone.

Tools necessary to reconstruct clonal affiliations from
temporally and/or spatially separated measurements of viral
integration sites. For this means it utilizes correlations present
in the relative readouts of the integration sites. Furthermore,
facilities for filtering of the data and visualization of different
steps in the pipeline are provided with the package.

normalize_timecourse: Normalizes a time course using a given mapping from integration sites to clones.

Description

Usage

Arguments

Value