Open cpmzwj opened 5 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.
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"
@FM-Jewl, we will address these concerns in Issue #6
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