coMET is an R-based package to visualize the EWAS (epigenome-wide association scans) results in a genomic region of interest. coMET diplays the strength of phenotype-methylation associations in a selected genomic region, together with the methylation correlation structure between CpG sites in the region, and a series of annotation features. Overall, the coMET package generates multi-panel plots of EWAS association signals, co-methylation patterns, and a series of annotation tracks at genomic scale.

The current version of coMET has two main functions. The function 'comet.web' plots using the default settings which are preformatted for the web service. The function 'comet' generates plot where the user can customize a new list of annotation tracks defined by the bioconductor package GViz.

IMAGES

Two example plots are shown below from different regions.

  • GATA4 data can be downloaded here. You can find here the files of version 1 of coMET (version related to the publication of paper in BMC bioinformatics)
  • an image

    Fig 1. Regional plot of the EWAS results and co-methylation patterns at the GATA4 gene. Methylation 450k data were obtained from the publicly available dataset of 648 adipose samples (Grundberg et al., AJHG 2013).

  • CYP1B1 data can be downloaded here. You can find here the files of version 1 of coMET (version related to the publication of paper in BMC bioinformatics)
  • an image

    Fig 2.Regional plot of the EWAS results,co-methylation pattern and gene expression on the GATA4 gene. Methylation 450k data were obtained from the publicly available dataset of 648 adipose tissues (Grundberg et al., AJHG 2013)

coMET help
Format of info file(mandatory):

The info file can be a list of CpG sites with/without Beta (or direction sign). If it is a CpG-site file then it is mandatory to have 4 columns as shown below with headers in the same order. The beta or direction can be included in the 5th column (optional).


TargetID CHR MAPINFO Pval Beta
cg22248750 2 38294160 0.27 0.006
cg11656478 2 38297759 0.78 0.07

Alternatively, the info file can be region-based and if so, the region-based info file must have the 5 columns (see below) with headers in this order. The beta or direction can be included in the 6th column (optional).


TargetID CHR MAPINFO.Start MAPINFO.Stop Pval Beta
ENSG00000138061.7_38294652_38298453 2 38294652 38298453 0.00 +
ENSG00000138061.7_38301489_38302532 2 38301489 38302532 0.01 +


Format of correlation matrix(mandatory):

The correlation matrix dataset can either be a pre-calculated correlation matrix or the raw data. If it is a raw data then you can select the type of correlation method (spearman, kendall or pearson).


cg11656478 cg14407177 cg02162897 cg20408276 cg00565882
-0.09 -0.49 1.67 0.52 0.17
-0.00 -0.63 0.32 -0.30 -0.43

Format of extra info file:

This can be another type of info file (e.g Expression data or replication data).