I tried to analyze A/B compartment with minfi. Since My data is annotated with hg38, but makeGenomicRatioSetFromMatrix
accept only hg19, I used liftOver function. But I got following error under this situation.library(rtracklayer) chain=import.chain("/Volumes/Crucial X6/PRJNA218851/hg19ToHg38.over.chain") GRset <- makeGenomicRatioSetFromMatrix(mat = betas.matrix, array = "IlluminaHumanMethylation450k", annotation = "ilmn12.hg19", what = "Beta") GRset_hg38 <- liftOver(GRset,chain) Error in { : task 1 failed - "is(object, "SummarizedExperiment") is not TRUE" Also I converted my object to SummarizedExperiment, but I still have following error. object is of class 'RangedSummarizedExperiment', but needs to be of class 'GenomicMethylSet' or 'GenomicRatioSet Do you know some solution for this analysis with hg38?
I tried to analyze A/B compartment with minfi. Since My data is annotated with hg38, but makeGenomicRatioSetFromMatrix accept only hg19, I used liftOver function. But I got following error under this situation.
library(rtracklayer) chain=import.chain("/Volumes/Crucial X6/PRJNA218851/hg19ToHg38.over.chain") GRset <- makeGenomicRatioSetFromMatrix(mat = betas.matrix, array = "IlluminaHumanMethylation450k", annotation = "ilmn12.hg19", what = "Beta") GRset_hg38 <- liftOver(GRset,chain) Error in { : task 1 failed - "is(object, "SummarizedExperiment") is not TRUE"Also I converted my object to SummarizedExperiment, but I still have following error.object is of class 'RangedSummarizedExperiment', but needs to be of class 'GenomicMethylSet' or 'GenomicRatioSetDo you know some solution for this analysis with hg38?