MEDIPS.addCNV {MEDIPS} | R Documentation |
Function calculates a CNV analysis based on two INPUT SETs by employing the DNAcopy package. The results are attached to a provided result table.
MEDIPS.addCNV(ISet1, ISet2, results, cnv.Frame=1000)
ISet1 |
First group of INPUT SETs |
ISet2 |
Second group of INPUT SETs |
results |
result table as returned by the MEDIPS.meth function |
cnv.Frame |
window size used for calculating CNVs. Can be of different size than the result table. |
The result table with an additional column containing DNAcopy's log-ratio.
Joern Dietrich
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)