FourC {FourCSeq} | R Documentation

## FourC-class

### Description

FourC-class

### Usage

    ## S4 method for signature 'FourC'
    updateObject(object, ..., verbose = FALSE)

    FourC(colData, metadata)

### Arguments

`object` | Object of class `FourC`
`...` | Additional arguments
`verbose` | Logical indicating volumn of information shown
`colData` | Column data that contains the required information for each library to set up the `FourC` object: viewpoint, name of the viewpoint condition, experimental condition replicate, replicate number bamFile, file name of the bam file sequencingPrimer, was the 4C library sequenced from the side of the first restriction enzyme cutting site or second
`metadata` | Experimental data information required for the `FourC` object: projectPath, directory where the project will be saved fragmentDir, directory in the project directory where the information about restriction fragments will be saved referenceGenomeFile, path to the reference genome or a `BSgenome` object. reSequence1, restriction enzyme recognition pattern of the first restriction enzyme reSequence2, restriction enzyme recognition pattern of the second restriction enzyme primerFile, path to the file containing the primer sequences used for preparing the 4C libraries bamFilePath, path to the directory where the bam files are stored

### Note

The `FourC` object extends the `DESeqDataSet` class.

### Examples

    metadata <- list(projectPath=tempdir(),
                     fragmentDir="re_fragments",
                     referenceGenomeFile=system.file("extdata/dm3_2L_1-6900.fa",
                                                     package="FourCSeq"),
                     reSequence1="GATC",
                     reSequence2="CATG",
                     primerFile=system.file("extdata/primer.fa",
                                            package="FourCSeq"),
                     bamFilePath=system.file("extdata/bam", package="FourCSeq"))

    colData <- DataFrame(viewpoint = "testdata",
                         condition = factor(rep(c("WE_68h", "MESO_68h", "WE_34h"),
                                                each=2),
                                            levels = c("WE_68h", "MESO_68h", "WE_34h")),
                         replicate = rep(c(1, 2),
                                         3),
                         bamFile = c("CRM_ap_ApME680_WE_6-8h_1_testdata.bam",
                                     "CRM_ap_ApME680_WE_6-8h_2_testdata.bam",
                                     "CRM_ap_ApME680_MESO_6-8h_1_testdata.bam",
                                     "CRM_ap_ApME680_MESO_6-8h_2_testdata.bam",
                                     "CRM_ap_ApME680_WE_3-4h_1_testdata.bam",
                                     "CRM_ap_ApME680_WE_3-4h_2_testdata.bam"),
                         sequencingPrimer="first")

    fc <- FourC(colData, metadata)
    fc

[Package FourCSeq version 1.22.1 Index]