methVisual (version 1.24.0)

MethAlignNW: Summary of methylation states

Description

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

Usage

MethAlignNW(refSeq, QCdata, alignment)

Arguments

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

Value

Returns a summery on sequence alignments and methylation states

Details

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.

Examples

## 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)