MethylQC: Quality controle (QC) on Methylation Data

Description Usage Arguments Details Value Author(s) Examples

View source: R/MethylQC.R

Description

Processing a quality control (QC) procedure on bisulafite sequences

Usage

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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 <[email protected]>, Christine Steinhoff <[email protected]>

Examples

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## 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 May 2, 2018, 2:49 a.m.