importBasic4CseqData {Scale4C} | R Documentation

## Import raw data from a provided Basic4Cseq output file

### 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)

[Package Scale4C version 1.2.0 Index]