DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts

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

Permanent link to the paper

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

List the paper results concerning method comparison and benchmarking:

1.2.1 Outcome O1

The performance of ...

1.2.2 Outcome O2

...

1.2.3 Outcome On

...

1.2.4 Further outcomes

If intended, you can add further outcomes here.

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 ...
• ...

1.5 References

The list of cited or related literature is placed here.