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xiaowangCN / GeneDMRs

GeneDMRs is an R package to detect the differentially methylated regions based on genes, gene body, CpG islands and gene body interacted with CpG island features.
GNU Lesser General Public License v3.0
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Methmean_region() does not work for chrnum="all"? #3

Open at2e19 opened 1 year ago

at2e19 commented 1 year ago

Hello,

I am trying run DMR analysis on 19 whole-genome sequencing methylation data I have in the form of bed files. When I run the Methmean_region() with all chromosomes, it takes too long and my job runs until the maximum time limit I can set and ultimately fails as the job is not complete within the limit of 60 hours. Any suggestions as to what I can do to speed up this process?

Below is the code I am running:

List of tsv file

controls <- c() cases <- c()

read the methylation file

inputmethfile <- Methfile_read(control_paths=controls, case_paths=cases)

quality control

inputmethfile_QC <- Methfile_QC(inputmethfile, low_coveragenum=5, high_coveragenum = NULL, low_quantile= NULL, high_quantile = NULL, samplenum_QC = "all")

read the bedfile

inputrefseqfile <- Bedfile_read(paths = "/mainfs/cansci/Anna_Takeuchi/CEGX_quant/", bedfile = "refseq", suffix = ".txt", feature = TRUE) inputcpgifeaturefile <- Bedfile_read(paths = "/mainfs/cansci/Anna_Takeuchi/CEGX_quant/", bedfile = "cpgi", suffix = ".txt", feature = TRUE)

methylation mean

regiongeneall <- Methmean_region(inputmethfile_QC, inputrefseqfile, chrnum = "all")

Thanks

hliihbcas commented 1 year ago

I also encountered this problem, the calculation speed of Methmean_region is too slow. My data background is that the methylation rate data frame has 482,519,318 lines, and the annotation bed file has 142,133 lines. The speed of executing Methmean_region seems to be too slow. Does the author have fast calculation parameters or settings?