Update 10-bs-seq-analysis.Rmd

10-bs-seq-analysis.Rmd

@@ -18,7 +18,7 @@ The epigenome consists of chemical modifications of DNA and histones. These modi
 ## What is DNA methylation?
 Cytosine methylation (5-methylcytosine, 5mC) is one of the main covalent base modifications in eukaryotic genomes, generally observed on CpG dinucleotides. Methylation can also rarely occur in a non-CpG context, but this was mainly observed in human embryonic stem and neuronal cells [@Lister2009-sd; @Lister2013-vs]. DNA methylation is a part of the epigenetic regulation mechanism of gene expression. It is cell-type-specific DNA modification. \index{DNA methylation}It is reversible but mostly remains stable through cell division.  There are roughly 28 million CpGs in the human genome, 60–80% are generally methylated. Less than 10% of CpGs occur in CG-dense regions that are termed CpG islands in the human genome [@Smith2013-jh]. It has been demonstrated that DNA methylation is also not uniformly distributed over the genome, but rather is associated with CpG density. In vertebrate genomes, cytosine bases are usually unmethylated in CpG-rich regions such as CpG islands and tend to be methylated in CpG-deficient regions. Vertebrate genomes are largely CpG deficient except at CpG islands. Conversely, invertebrates such as _Drosophila melanogaster_ and _Caenorhabditis elegans_ do not exhibit cytosine methylation and consequently do not have CpG rich and poor regions but rather a steady CpG frequency over their genomes [@Deaton2011-pm]. 
 
-### How DNA methylation is set ?
+### How DNA methylation is set 
 DNA methylation is established by DNA methyltransferases DNMT3A and DNMT3B in combination with DNMT3L and maintained through cell division by the methyltransferase DNMT1 and associated proteins. DNMT3a and DNMT3b are in charge of the de novo methylation during early development. Loss of 5mC can be achieved passively by dilution during replication or exclusion of DNMT1 from the nucleus. Recent discoveries of the ten-eleven translocation (TET) family of proteins and their ability to convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) in vertebrates provide a path for catalyzed active DNA demethylation [@Tahiliani2009-ar]. Iterative oxidations of 5hmC catalyzed by TET result in 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). 5caC mark is excised from DNA by G/T mismatch-specific thymine-DNA glycosylase (TDG), which as a result reverts cytosine residue to its unmodified state [@He2011-pw]. Apart from these, mainly bacteria, but possibly higher eukaryotes, contain base modifications on bases other than cytosine, such as methylated adenine or guanine [@Clark2011-sc].
 
 ### How to measure DNA methylation with bisulfite sequencing
@@ -66,7 +66,7 @@ tab
 Most of the time bisulfite sequencing experiments have test and control  samples. The test samples can be from a disease tissue while the control  samples can be from a healthy tissue. You can read a set of methylation call files that have test/control conditions giving a `treatment` vector option. The treatment vector defines the sample groups and it is very important for the differential methylation analysis. For the sake of subsequent analysis, file.list, sample.id and treatment option should have the same order. In the following example, the first two files have the sample IDs "test1" and "test2" and as determined by the treatment vector they belong to the same group. The third and fourth files have sample IDs "ctrl1" and "ctrl2" and they belong to the same group as indicated by the treatment vector. We will first get a list of file paths and have a look at the content.
 
 
-```{r readMethFiles,message=FALSE,echo=FALSE}
+```{r readMethFiles,message=FALSE,echo=TRUE}
 library(methylKit)
 file.list=list( system.file("extdata", 
                             "test1.myCpG.txt", package = "methylKit"),