MethAlignNW: Summary of methylation states
In methVisual: Methods for visualization and statistics on DNA methylation data

Description Usage Arguments Details Value Author(s) Examples

Summarize the methylation states after calculating pairwise alignments of each examined sequences and the genomic sequence

1	MethAlignNW(refSeq, QCdata, alignment)

`refSeq`	String; Genomic sequence as String format
`QCdata`	Data frame; Names and paths of analysed sequences after quality control
`alignment`	If TRUE, alignments are included in summery, else not included

Given aligned sequences after quality control, the function returns a list object with the following data: sequences name, methylation state on CpG position, start and end position of alignments and length of genomic sequence. The data includes the core information for the exploratory analysis and visualizations.

Returns a summery on sequence alignments and methylation states

Arie Zackay <arie.zackay@mail.huji.ac.il>, Christine Steinhoff <steinhof@molgen.mpg.de>

## In order to use the following example 
## make sure that you have writing permission under R.home()
## directory. If you do not have permission choose your own path. 
#dir.create(file.path(R.home(component="home"),"/BiqAnalyzer"))
BiqAnalyzer_path <- file.path(tempdir(), "BiqAnalyzer")
dir.create(BiqAnalyzer_path) 
makeLocalExpDir(dataPath="/examples/BiqAnalyzer", localDir=BiqAnalyzer_path)
datameth <- MethDataInput(file.path(BiqAnalyzer_path, "PathFileTab.txt"))
refseq <- selectRefSeq(file.path(BiqAnalyzer_path, "Master_Sequence.txt"))
QCdata <- MethylQC(refseq, datameth)
methData <- MethAlignNW( refseq , QCdata)