Difference between revisions of "DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts"
(Created page with "__NUMBEREDHEADINGS__ == DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts == Cato...") |
(→DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts) |
||
| Line 5: | Line 5: | ||
DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts. Nucleic Acids Res. 2018 Nov 2;46(19):e114 | DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts. Nucleic Acids Res. 2018 Nov 2;46(19):e114 | ||
| − | [https://doi.org/10.1093/nar/gky602 | + | [https://doi.org/10.1093/nar/gky602 Permanent link to the paper] |
| Line 17: | Line 17: | ||
=== Study outcomes === | === Study outcomes === | ||
| − | + | ||
==== Outcome O1 ==== | ==== Outcome O1 ==== | ||
| − | The performance of | + | The performance of DMR-caller-B and DMR-caller-NF is superior to methlySig and methylKit |
==== Outcome O2 ==== | ==== Outcome O2 ==== | ||
| Line 28: | Line 28: | ||
==== Further outcomes ==== | ==== Further outcomes ==== | ||
| − | + | Boxplots for the run-times of DMRcaller−B, DMRcaller−NF, MethylKit, MethylSig, MethylPipe are provided. MithylKit and MethylSig are fastest. | |
| − | |||
=== Study design and evidence level === | === Study design and evidence level === | ||
==== General aspects ==== | ==== General aspects ==== | ||
| + | |||
You can describe general design aspects here. | You can describe general design aspects here. | ||
The study designs for describing specific outcomes are listed in the following subsections: | The study designs for describing specific outcomes are listed in the following subsections: | ||
| Line 53: | Line 53: | ||
=== Further comments and aspects === | === Further comments and aspects === | ||
| + | The choice for using methylSig and methylKit as reference is that only these tools (and methylPipe) can handle non-CpG sequence contexts. | ||
=== References === | === References === | ||
| − | + | ||
| + | [http://bioconductor.org/packages/DMRcaller DMRcaller Bioconductor package] | ||
| + | |||
| + | [https://github.com/al2na/methylKit methylKit package on github ] | ||
| + | |||
| + | [https://github.com/sartorlab/methylSig methylSig package on github] | ||
| + | |||
| + | [http://bioconductor.org/packages/methylPipe methylPipe Bioconductor package] | ||
Revision as of 16:02, 22 January 2019
Contents
1 DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts
Catoni M, Tsang JM, Greco AP, Zabet NR DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts. Nucleic Acids Res. 2018 Nov 2;46(19):e114
1.1 Summary
The paper considers identification of differentially methylated regions (DMRs) from bisulfite sequencing data (BSSEQ). A new package is introduced. The package allows choosing between three approaches (individual cytosines, pooled tiling-intervals or smoothed data) for merging data from individuals cytosines. Several test statistics can be chosen (Fisher's Exact test, score-test, beta regression). Differential positions/bins/regions are selected based on three requirements: p-value<threshold, methylation difference>threshold, coverage>threshold.
Publicly available data from Arabidopsis thaliana,rice and human cell lines was analyzed.
The performance of the presented approach was assessed by comparing with three other methods (methylKit, methylSig and methylPipe).
1.2 Study outcomes
1.2.1 Outcome O1
The performance of DMR-caller-B and DMR-caller-NF is superior to methlySig and methylKit
1.2.2 Outcome O2
...
1.2.3 Outcome On
...
1.2.4 Further outcomes
Boxplots for the run-times of DMRcaller−B, DMRcaller−NF, MethylKit, MethylSig, MethylPipe are provided. MithylKit and MethylSig are fastest.
1.3 Study design and evidence level
1.3.1 General aspects
You can describe general design aspects here. The study designs for describing specific outcomes are listed in the following subsections:
1.3.2 Design for Outcome O1
- The outcome was generated for ...
- Configuration parameters were chosen ...
- ...
1.3.3 Design for Outcome O2
- The outcome was generated for ...
- Configuration parameters were chosen ...
- ...
...
1.3.4 Design for Outcome O
- The outcome was generated for ...
- Configuration parameters were chosen ...
- ...
1.4 Further comments and aspects
The choice for using methylSig and methylKit as reference is that only these tools (and methylPipe) can handle non-CpG sequence contexts.
