addPointsOfInterest: Add points of interest to a 'Scale4C' object

In Scale4C: Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data

Description

The function addPointsOfInterest adds marker points to a Scale4C object, which are subsequently used to mark points of interest in created plots.

Usage

addPointsOfInterest(data, poi)

Arguments

data	Scale4C object the points are to be added to
poi	Points of interest data, in a GRanges object. Important: column names must be specified and include 'colour' and 'name' for each point of interest with appropriate values

Details

The function addPointsOfInterest adds predefined points of interest to a Scale4C object. Each point of interest is defined by 'chr', 'start', 'end', 'colour', and 'name'. A bed file or text file can be used to store the information, however, column names have to be added before import. Other additional columns are ignored by the function. The function then converts the information to a GRanges object.

Value

A data frame that contains the data for all points of interest

Author(s)

Carolin Walter

Examples

    # import provided point of interest example, and check if import was 
    # successful
    data(liverData)
    poiFile <- system.file("extdata", "vp.txt", package="Scale4C")
    pointsOfInterest(liverData) <- addPointsOfInterest(liverData, 
        read.csv(poiFile, sep = "\t", stringsAsFactor = FALSE))
    head(pointsOfInterest(liverData))

Scale4C documentation built on Nov. 8, 2020, 8:21 p.m.