Function to run a copy number variation analysis.

Description

Function calculates a CNV analysis based on two INPUT SETs by employing the DNAcopy package. The results are attached to a provided result table.

Usage

MEDIPS.addCNV(ISet1, ISet2, results, cnv.Frame=1000)

Arguments

Value

The result table with an additional column containing DNAcopy's log-ratio.

Author(s)

Joern Dietrich

Examples

library(MEDIPSData)
library("BSgenome.Hsapiens.UCSC.hg19")

bam.file.hESCs.Input = system.file("extdata", "hESCs.Input.chr22.bam", package="MEDIPSData")
bam.file.DE.Input = system.file("extdata", "DE.Input.chr22.bam", package="MEDIPSData")

hESCs.Input = MEDIPS.createSet(file=bam.file.hESCs.Input, BSgenome="BSgenome.Hsapiens.UCSC.hg19", extend=250, shift=0, uniq=1e-3, window_size=100, chr.select="chr22")
DE.Input = MEDIPS.createSet(file=bam.file.DE.Input, BSgenome="BSgenome.Hsapiens.UCSC.hg19", extend=250, shift=0, uniq=1e-3, window_size=100, chr.select="chr22")

data(resultTable)

resultTable = MEDIPS.addCNV(cnv.Frame=10000, ISet1=hESCs.Input, ISet2=DE.Input, results=resultTable)

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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> library(MEDIPS)
Loading required package: BSgenome
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: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MEDIPS/MEDIPS.addCNV.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MEDIPS.addCNV
> ### Title: Function to run a copy number variation analysis.
> ### Aliases: MEDIPS.addCNV
> 
> ### ** Examples
> 
> library(MEDIPSData)
> library("BSgenome.Hsapiens.UCSC.hg19")
> 
> bam.file.hESCs.Input = system.file("extdata", "hESCs.Input.chr22.bam", package="MEDIPSData")
> bam.file.DE.Input = system.file("extdata", "DE.Input.chr22.bam", package="MEDIPSData")
> 
> hESCs.Input = MEDIPS.createSet(file=bam.file.hESCs.Input, BSgenome="BSgenome.Hsapiens.UCSC.hg19", extend=250, shift=0, uniq=1e-3, window_size=100, chr.select="chr22")
Reading bam alignment hESCs.Input.chr22.bam 
Selecting  chr22 
Total number of imported short reads: 111515
Extending reads...
Creating GRange Object...
Keep at most 1 read(s) mapping to the same genomic location
Number of remaining reads: 110948
Calculating genomic coordinates...
Creating Granges object for genome wide windows...
Calculating short read coverage at genome wide windows...
> DE.Input = MEDIPS.createSet(file=bam.file.DE.Input, BSgenome="BSgenome.Hsapiens.UCSC.hg19", extend=250, shift=0, uniq=1e-3, window_size=100, chr.select="chr22")
Reading bam alignment DE.Input.chr22.bam 
Selecting  chr22 
Total number of imported short reads: 232344
Extending reads...
Creating GRange Object...
Keep at most 1 read(s) mapping to the same genomic location
Number of remaining reads: 230977
Calculating genomic coordinates...
Creating Granges object for genome wide windows...
Calculating short read coverage at genome wide windows...
> 
> data(resultTable)
> 
> resultTable = MEDIPS.addCNV(cnv.Frame=10000, ISet1=hESCs.Input, ISet2=DE.Input, results=resultTable)
Reading bam alignment hESCs.Input.chr22.bam 
Selecting  chr22 
Total number of imported short reads: 111515
Extending reads...
Creating GRange Object...
Keep at most 1 read(s) mapping to the same genomic location
Number of remaining reads: 110948
Calculating genomic coordinates...
Creating Granges object for genome wide windows...
Calculating short read coverage at genome wide windows...
Reading bam alignment DE.Input.chr22.bam 
Selecting  chr22 
Total number of imported short reads: 232344
Extending reads...
Creating GRange Object...
Keep at most 1 read(s) mapping to the same genomic location
Number of remaining reads: 230977
Calculating genomic coordinates...
Creating Granges object for genome wide windows...
Calculating short read coverage at genome wide windows...
Calculating genomic coordinates...
Creating Granges object for genome wide windows...
CNV analysis...
Analyzing: ISets.mean 
  current chromosome: chr22 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>