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lissettegomez / coMethDMR

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Where could find pre-defined genomic regions for EPIC array? #1

Open cpmzwj opened 4 years ago

lxw391 commented 4 years ago

Hi -- thanks for your interests in our package. We're currently working on annotations for the EPIC arrays and expect to release a new version in the next couple weeks. Please check back soon

lxw391 commented 4 years ago

Dear coMethDMR user,

We've now updated coMethDMR repository to include EPIC arrays annotation. Please refer to the updated vignettes in directory /docs. In particular, section 5 of the vignette " 2_BiocParallel_for_coMethDMR_geneBasedPipeline.pdf" describes annotation files to be used for EPIC datasets.

Let us know if you have any additional issues.

FM-Jewl commented 3 years ago

Dear professor, when I use the package on server, I always came with the error"Error in CoMethAllRegions(dnam = betasChr22_df, betaToM = TRUE, CpGs_ls = CpGisland_ls，could not find function ...“. It would be much appropriate if you can teach me about this. Thank you in advance. The following is the log:

library(coMethDMR) Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Registered S3 methods overwritten by 'lme4': method from cooks.distance.influence.merMod car influence.merMod car dfbeta.influence.merMod car dfbetas.influence.merMod car data(betasChr22_df) data(pheno_df) CpGisland_ls <- readRDS(

  • system.file (
  • "extdata",
  • "CpGislandsChr22_ex.RDS",
  • package = 'coMethDMR',
  • mustWork = TRUE
  • ) ) coMeth_ls <- CoMethAllRegions (
  • dnam = betasChr22_df,
  • betaToM = TRUE, #converts to mvalues
  • CpGs_ls = CpGisland_ls,
  • arrayType = "450k",
  • returnAllCpGs = FALSE,
  • output = "CpGs"
  • ) Error in CoMethAllRegions(dnam = betasChr22_df, betaToM = TRUE, CpGs_ls = CpGisland_ls, : could not find function "CoMethAllRegions"
gabrielodom commented 3 years ago

@FM-Jewl, we will address these concerns in Issue #6