search

lijingya / ELMER

Enhancer Linking by Methylation/Expression Relationship (ELMER) is package to identify tumor-specific changes in DNA methylation within distal enhancers, and link these enhancers to downstream target genes
6 stars 16 forks source link

Error in createMAE() #18

Open sumitpaliwal opened 5 years ago

sumitpaliwal commented 5 years ago

I was trying the ELMER pipeline with the TCGA-PAAD data as given here . However, I encountered the following error:

> distal.probes <- get.feature.probe(genome = "hg38", met.platform = "450K")
Downloading transcripts information. Using: Human genes (GRCh38.p12)
Returning distal probes: 160356
> library(MultiAssayExperiment)
> mae <- createMAE(exp = paad.exp, met = paad.met, save = TRUE, linearize.exp = TRUE, 
+                  filter.probes = distal.probes, save.filename = "mae_paad.rda",
+                  met.platform = "450K", genome = "hg38", TCGA = TRUE)
Downloading genome information (try:0) Using: Human genes (GRCh38.p12)
Error in createMAE(exp = paad.exp, met = paad.met, save = TRUE, linearize.exp = TRUE,  : 
  Please the gene expression matrix should receive ENSEMBLE IDs

How to resolve this issue? Thanks. Sumit