TrepDF

Trep is median replication time, expressed in minutes after release G1 arrest.
It is calculated from multiple relative copy number datapoints across timeseries
of a cell cycle experiment. For every genomic bin, a sigmoid function is fitted
and its midpoint is reported.

datasets

syncSeq

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

TrepDF function

data frame with 11341 rows and 5 variables:<dl>
	<dt>chrom</dt>
<dd>short chromosome name</dd>	<dt>chromStart</dt>
<dd>left chromosome coordinate</dd>	<dt>chromEnd</dt>
<dd>right chromosome coordinate</dd>	<dt>Trep</dt>
<dd>calculated Trep value</dd>	<dt>TrepErr</dt>
<dd>error from sigmoid function fitting</dd>
</dl>

Format

Trep data calculated from syncSeq[["data"]] — TrepDF

data frame with 11341 rows and 5 variables:<dl>
	<dt>chrom</dt>
<dd>short chromosome name</dd>

	<dt>chromStart</dt>
<dd>left chromosome coordinate</dd>

	<dt>chromEnd</dt>
<dd>right chromosome coordinate</dd>

	<dt>Trep</dt>
<dd>calculated Trep value</dd>

	<dt>TrepErr</dt>
<dd>error from sigmoid function fitting</dd>


</dl>

TrepDF: Trep data calculated from syncSeq[["data"]]

Description

Usage

Arguments

Format

References

Examples