Entering edit mode
11 months ago
Aki
▴
20
Hi, I am trying to A/B compartment analysis with minfi, but I got following error.
Error in { :
task 1 failed - "is(object, "SummarizedExperiment") is not TRUE"
Since I want to use data with hg38 annotation but makeGenomicRatioSetFromMatrix
function has only ilmn12.hg19
, I did makeGenomicRatioSetFromMatrix
function with ilmn12.hg19
and liftOver with hg19ToHg38.over.chain
which I get in UCSC, and did compartment analysis as below.
library(rtracklayer)
library(minfi)
chain=import.chain("hg19ToHg38.over.chain")
GRset <- makeGenomicRatioSetFromMatrix(mat = betas.matrix, # I got betas.matrix by "TCGAbiolinks" function
array = "IlluminaHumanMethylation450k",
annotation = "ilmn12.hg19",
what = "Beta")
GRset_hg38 <- liftOver(GRset,chain)
compartments_list <- foreach(chr = 1:22, .packages = "minfi") %dopar% {
compartments_result <- compartments(GRset_hg38, chr = paste0("chr", chr), what = "OpenSea", resolution = 100 * 1000)
}
Since makeGenomicRatioSetFromMatrix
function creates the object GRangesList
, but I got the object CompressedGRangesList
after liftOver, I suggest it could work if I use GRangesList
. But I don't know how to convert. Does anybody know the solution? Thanks.
It's asking for a
SummarizedExperiment
which is a separate object type from GenomicRanges. See the documentation for more information.Thanks, rpolicastro. I convert object type to SummarizedExperiment, but I got following error. but I don't have idea to getting class 'GenomicMethylSet' or 'GenomicRatioSet' of my dataset.