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

In Repliscope: Replication Timing Profiling using DNA Copy Number

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

Description

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.

Usage

data(TrepDF)

Format

data frame with 11341 rows and 5 variables:

chrom

short chromosome name

chromStart

left chromosome coordinate

chromEnd

right chromosome coordinate

Trep

calculated Trep value

TrepErr

error from sigmoid function fitting

References

Müller et al. (2014) NAR 42(1):e3 (PubMed)

Examples

data(TrepDF)

Repliscope documentation built on Sept. 13, 2022, 9:05 a.m.