importBasic4CseqData: Import raw data from a provided Basic4Cseq output file

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

Description

A convenience function to easily include Basic4Cseq output data into Scale4C, importBasic4CseqData extracts valid fragments or valid fragment ends from a typical Basic4Cseq output table.

Usage

importBasic4CseqData(rawFile, viewpoint, viewpointChromosome, 
    distance, useFragEnds = TRUE)

Arguments

rawFile	Name for the raw file
viewpoint	Viewpoint position: only fragments around a certain point of interest are imported (doesn't have to be the actual viewpoint of the experiment, though)
viewpointChromosome	Viewpoint chromosome of the experiment
distance	Distance from the viewpoint: ony fragments within a certain distance of the viewpoint are imported
useFragEnds	If TRUE, use full fragment end data, if FALSE, merge fragmentStart and fragmentEnd to a single item per fragment

Details

importBasic4CseqData is a convenience function to import data from Basic4Cseq. It can be ignored altogether if raw experimental data is imported from another source or with another function into R.

Value

A GRanges object that includes the experiment's raw data for further processing

Author(s)

Carolin Walter

Examples

    csvFile <- system.file("extdata", "liverData.csv", package="Scale4C")
    liverReads <- importBasic4CseqData(csvFile, viewpoint = 21160072, 
                viewpointChromosome = "chr10", distance = 1000000)
    head(liverReads)

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