FourC object with counts

Description

This file contains the FourCSeq object fc. The reference fragments have been added and the overlaps of the reference fragments and aligned reads were counted. (See ?addFragments or the vignette of the 'FourCSeq' package for details).

Usage

data(fc)

Format

Formal class 'FourC' [package "FourCSeq"]

Examples

data(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/fc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: fc
> ### Title: FourC object with counts
> ### Aliases: fc
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(fc)
> fc
class: FourC 
dim: 57253 6 
metadata(7): projectPath fragmentDir ... primerFile bamFilePath
assays(3): counts countsLeftFragmentEnd countsRightFragmentEnd
rownames: NULL
rowData names(4): leftSize rightSize leftValid rightValid
colnames(6): ap_WE_68h_1 ap_WE_68h_2 ... ap_WE_34h_1 ap_WE_34h_2
colData names(21): viewpoint condition ... mappedReads mappingRatio
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>