makeGenome: A helper function to create a gemome dataframe

In Repliscope: Replication Timing Profiling using DNA Copy Number

A helper function to create a gemome dataframe

Description

makeGenome is called by plotGenome() and plotCoverage() functions if a genome dataframe is not provided. It creates a BED-like dataframe containing unique chromosome names, their start coordinates (assumed 0), their ends (highest value in the corresponding 'chromEnd' of the BED dataframe) and 'midY' column containing half the max value of the "score" or "ratio" columns per chromosome. This later serves as y coordinate to add chromosome names. Axis name is passed via comment to the output dataframe. Extract it with 'attributes(genome)$axisName'.

Usage

makeGenome(DF, region = FALSE)

Arguments

DF	A BED or ratio dataframe containing either 'score' or 'ratio' column (dataframe).
region	String in the format 'chrI:1000-3000' (string, optional).

Examples

genomeDF <- makeGenome(W303_G2)

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