Add the information of the viewpoint fragments

Description

addViewpointFrags adds the genomic position and information of the viewpoint primer fragments to colData of the FourC object.

Usage

addViewpointFrags(object, primerFragFile)

Arguments

Value

Updated FourC object with information about the viewpoint fragments added to colData.

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)

findViewpointFragments(fc)

fc <- addViewpointFrags(fc)
fc

Results

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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/addViewpointFrags.Rd_%03d_medium.png", width=480, height=480)
> ### Name: addViewpointFrags
> ### Title: Add the information of the viewpoint fragments
> ### Aliases: addViewpointFrags
> 
> ### ** 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)
> 
> findViewpointFragments(fc)
> 
> fc <- addViewpointFrags(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(16): viewpoint condition ... primerEnd primerSide
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>