calcTrep

A function to calculate Trep values from a sync-seq experiment
calcTrep function fits a Boltzman sigmoid function into relative copy number datapoints for every
genomic bin of the provided sync-seq merged dataframe. It then extracts time at which half of the
cells have this genomic bin replicated (Trep). The output of the function is a dataframe containing
Trep and TrepErr data for every genomic bin in a BED-like format.

Bioinformatics

replication

sigmoid

genomics

Trep

Create, Plot and Compare Replication Timing Profiles. The method is described in Muller et al., (2014) <doi: 10.1093/nar/gkt878>.

Dzmitry Batrakou

Repliscope

Replication Timing Profiling using DNA Copy Number

calcTrep function

<dl><dt>ratioDFs</dt>
<dd>A merged ratios dataframe containing sync-seq samples (dataframe).</dd>
<dt>times</dt>
<dd>Time series data in the same order as in the ratioDFs (numeric vector).</dd></dl>

Arguments

A function to calculate Trep values from a sync-seq experiment
calcTrep function fits a Boltzman sigmoid function into relative copy number datapoints for every
genomic bin of the provided sync-seq merged dataframe. It then extracts time at which half of the
cells have this genomic bin replicated (Trep). The output of the function is a dataframe containing
Trep and TrepErr data for every genomic bin in a BED-like format. — calcTrep

<dl>

<dt>ratioDFs</dt>
<dd>A merged ratios dataframe containing sync-seq samples (dataframe).</dd>


<dt>times</dt>
<dd>Time series data in the same order as in the ratioDFs (numeric vector).</dd>

</dl>

A function to calculate Trep values from a sync-seq experiment
calcTrep function fits a Boltzman sigmoid function into relative copy number datapoints for every
genomic bin of the provided sync-seq merged dataframe. It then extracts time at which half of the
cells have this genomic bin replicated (Trep). The output of the function is a dataframe containing
Trep and TrepErr data for every genomic bin in a BED-like format.

Description

Usage

Arguments

Examples