FourC-class

Description

FourC-class

Usage

1
FourC(colData, metadata)

Arguments

colData

Column data that contains the required information for each library to set up the FourC object:

  1. viewpoint, name of the viewpoint

  2. condition, experimental condition

  3. replicate, replicate number

  4. bamFile, file name of the bam file

  5. 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:

  1. projectPath, directory where the project will be saved

  2. fragmentDir, directory in the project directory where the information about restriction fragments will be saved

  3. referenceGenomeFile, path to the reference genome or a BSgenome object.

  4. reSequence1, restriction enzyme recognition pattern of the first restriction enzyme

  5. reSequence2, restriction enzyme recognition pattern of the second restriction enzyme

  6. primerFile, path to the file containing the primer sequences used for preparing the 4C libraries

  7. bamFilePath, path to the directory where the bam files are stored

Note

The FourC object extends the DESeqDataSet class.

Examples

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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