methylationDataList


A <code>GRangesList</code> object containing the methylation data at each cytosine
location in the genome in  Wild Type (WT) and  met1-3 mutant (met1-3) in
Arabidopsis thaliana. The data only contains the first 1 Mbp from Chromosome 3.


Uses Bisulfite sequencing data in two conditions and
identifies differentially methylated regions between the
conditions in CG and non-CG context. The input is the CX report
files produced by Bismark and the output is a list of DMRs
stored as GRanges objects.

Nicolae Radu Zabet

DMRcaller

Differentially Methylated Regions caller

methylationDataList function

The <code>GRanges</code> elements contain four metadata columns
<dl>
 <dt>context</dt><dd>the context in which the DMRs are computed (<code>"CG"</code>,
               <code>"CHG"</code> or <code>"CHH"</code>).</dd> <dt>readsM</dt><dd>the number of methylated reads.</dd> <dt>readsN</dt><dd>the total number of reads.</dd> <dt>trinucleotide_context</dt><dd>the specific context of the cytosine (H is
                             replaced by the actual nucleotide).</dd> </dl>

Format

Each element was created by by calling <code><a rd-options="" href="/link/readBismark?package=DMRcaller&version=1.4.2" data-mini-rdoc="DMRcaller::readBismark">readBismark</a></code>
function on the CX report files generated by Bismark
<a href="http://www.bioinformatics.babraham.ac.uk/projects/bismark/">http://www.bioinformatics.babraham.ac.uk/projects/bismark/</a>
for <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM980986">http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM980986</a> dataset
in the case of Wild Type (WT) and
<a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM981032">http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM981032</a>
dataset in the case of met1-3 mutant (met1-3).

Source

A <code>GRangesList</code> object containing the methylation data at each cytosine
location in the genome in  Wild Type (WT) and  met1-3 mutant (met1-3) in
Arabidopsis thaliana. The data only contains the first 1 Mbp from Chromosome 3.

methylationDataList: The methylation data list

Description

Arguments

Format

Source