calcTrep: A function to calculate Trep values from a sync-seq...

In Repliscope: Replication Timing Profiling using DNA Copy Number

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

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.

Usage

calcTrep(ratioDFs, times)

Arguments

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

Examples

TrepDF <- calcTrep(subset(syncSeq[["data"]],chrom=="chrI"),times=c(25,30,35,40,45,50,90))

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