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TiphaineCMartin / coMET_original

The coMET package is a web-based plotting tool and R-based package to visualize different genome-wide association scans such as EWAS (epigenome-wide association scan) results in a genomic region of interest. coMET provides a plot of the EWAS association signal and visualisation of the methylation correlation between CpG sites (co-methylation). The coMET package also provides the option to annotate the region using functional genomic information, including both user-defined features and pre-selected features based on the Encode project. The plot can be customized with different parameters, such as plot labels, colours, symbols, heatmap colour scheme, significance thresholds, and including reference CpG sites. Finally, the tool can also be applied to display the correlation patterns of other genomic data, e.g. gene expression array data.
GNU General Public License v2.0
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error for coMET #2

Open weizhousjtu opened 5 years ago

weizhousjtu commented 5 years ago

Hi, I got an error: Error in unit(at, "native") : 'x' and 'units' must have length > 0 when I run some DMR, but other DMR normal running. I check the file and found no error. It seems random. Look forward to your reply.

TiphaineCMartin commented 5 years ago

more often the issue is in the writing of files. Could you share with me your files and configuration? please you can modify pvalue and correlation matrice if you want. (this is my email: tiphaine.martin_at_mssm.edu)

weizhousjtu commented 5 years ago

Thank you for your reply! I carefully checked my file and I found the configuration file included CpG site that not in my correlation file. Now the problem solved. Another question is no annotation figure legends when using comet function. However, comet.web function show the annotation figure legends. Any suggestions? Attachment is my file. I am looking forward to your reply!

发件人: TMartin 发送时间: 2019年11月8日 1:27 收件人: TiphaineCMartin/coMET_original 抄送: WeiZhou; Author 主题: Re: [TiphaineCMartin/coMET_original] error for coMET (#2)

more often the issue is in the writing of files. Could you share with me your files and configuration? please you can modify pvalue and correlation matrice if you want. (this is my email: tiphaine.martin_at_mssm.edu) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

TiphaineCMartin commented 5 years ago

Great that you find why it did not work in the first time! for the annotation, unfortunately I did not find the way to write efficiently the name of annotation tracks in the function "comet" as I did with "comet.web", because there are more variables to take care and people can add their own annotation tracks. Moreover, most of the time my collaborators modified them before publication. So we decide that it was better to not add it if using "comet" and people need to modify their own pdf.