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YuanTian1991 / ChAMP

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champ.filter Filtering probes on EPICv1 #40

Open robinjugas opened 10 months ago

robinjugas commented 10 months ago

Hi, I think because of updates, the filtering of probes on EPIC V1 ceased to stop working. It happens both with champ.import+champ.filter and champ.load(with filtering)

myLoadEPICV1 <- champ.import(directory = testDir, arraytype="EPICv1"
myLoadEPICV1 <- champ.filter(beta=myLoadEPICV1$beta,
  M=myLoadEPICV1$M,
  pd=myLoadEPICV1$pd,
  autoimpute=FALSE,
  filterDetP=TRUE,
  filterSNPs = TRUE,
  filterXY = TRUE,
  arraytype = "EPICv1")

Filtering XY Start Error in champ.filter(beta = myLoadEPICV1$beta, M = myLoadEPICV1$M, pd = myLoadEPICV1$pd, : object 'probe.features' not found In addition: Warning message: In data("probe.features.epicv1") : data set 'probe.features.epicv1' not found

The EPICv2 chips are processed fine. Best regards, Robin

robinjugas commented 10 months ago

Renaming the probe.features.epic.rda to probe.features.epicv1.rda in ChampData package solved this.