MethylQC: Quality controle (QC) on Methylation Data

In methVisual: Methods for visualization and statistics on DNA methylation data

Description

Processing a quality control (QC) procedure on bisulafite sequences

Usage

MethylQC(refSeq, methFileDataFrame, makeChange, identity,conversion)

Arguments

refSeq	String; genomic sequence, see selectRefSeq()
methFileDataFrame	Data frame; sequences names and their paths, see MethDataInput()
makeChange	Logical; if TRUE changes take place automatically, by default TRUE
identity	min. identity value , by default 80 percent
conversion	min conversion rate, by default 90 percent

Details

In order to avoid bad qualitative data entering this methylation analysis three measurements are made: 1) alignment check: if reverse, complement or reverse-complement 2) sequence identity between genomic sequence and every examined sequence 3) bisulfite conversion

Value

Returns data frame of sequences names after QC and their paths saves QCINFO.Rdata under sequence files directory

Author(s)

Arie Zackay <[e-mail]>, Christine Steinhoff <[e-mail]>

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)

methVisual documentation built on April 28, 2020, 7:08 p.m.