Add the restriction fragment information

Description

addFragments adds the genomic position and information of the restriction fragments as GRanges object to rowRanges of the FourC object.

Usage

addFragments(object, minSize = 20, filter = TRUE, save = FALSE)

Arguments

Value

Updated FourC object that contains the information about the restriction fragments in rowRanges.

Author(s)

Felix A. Klein, felix.klein@embl.de

See Also

FourC, findViewpointFragments

Examples

metadata <- list(projectPath=tempdir(),
                 fragmentDir="re_fragments",
                 referenceGenomeFile=system.file("extdata/dm3_chr2L_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

fc <- addFragments(fc)
fc

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/addFragments.Rd_%03d_medium.png", width=480, height=480)
> ### Name: addFragments
> ### Title: Add the restriction fragment information
> ### Aliases: addFragments
> 
> ### ** Examples
> 
> metadata <- list(projectPath=tempdir(),
+                  fragmentDir="re_fragments",
+                  referenceGenomeFile=system.file("extdata/dm3_chr2L_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
> 
> fc <- addFragments(fc)
> fc
class: FourC 
dim: 2 6 
metadata(8): projectPath fragmentDir ... bamFilePath version
assays(0):
rownames: NULL
rowData names(4): leftSize rightSize leftValid rightValid
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 
>