Last data update: 2014.03.03

 R: FourC-class
FourCR Documentation

FourC-class

Description

FourC-class

Usage

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

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(FourCSeq)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Loading required package: DESeq2
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: splines
Loading required package: LSD
Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/FourCSeq/FourC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: FourC
> ### Title: FourC-class
> ### Aliases: FourC FourC-class updateObject,FourC-method
> ### Keywords: package
> 
> ### ** 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
class: FourC 
dim: 0 6 
metadata(8): projectPath fragmentDir ... bamFilePath version
assays(0):
rownames: NULL
rowData names(0):
colnames(6): testdata_WE_68h_1 testdata_WE_68h_2 ... testdata_WE_34h_1
  testdata_WE_34h_2
colData names(5): viewpoint condition replicate bamFile
  sequencingPrimer
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO