FourC: FourC-class

In FourCSeq: Package analyse 4C sequencing data

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
 

FourCSeq documentation built on Nov. 8, 2020, 7:08 p.m.