Created
December 14, 2022 15:16
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| ######### | |
| #Script running methylkit on the gold standard/aging data set | |
| ######### | |
| library(methylKit) | |
| library(bsseq) | |
| library(BiocParallel) | |
| library(here) | |
| library(data.table) | |
| library(stringr) | |
| mc_cores <- 30 | |
| register(MulticoreParam(mc_cores)) | |
| set.seed(0) | |
| # Define the directory of output | |
| output_dir <- here::here('results/Methylkit_aging') | |
| if (!dir.exist(output_dir)) dir.create(output_dir, recursive = TRUE) | |
| ############################################################################### | |
| ## Get Data | |
| ############################################################################### | |
| control_fname <- here::here('data/EGAZ00001016574_90_cpg.txt.gz') | |
| case_fname <- here::here('data/EGAZ00001016575_90_cpg.txt.gz') | |
| convert_data_format <- function(fname) { | |
| dt <- fread(fname) | |
| colnames <- names(dt) | |
| dt[, total_reads := get(colnames[8]) + get(colnames[9])] | |
| dt[, strand := '+'] | |
| fwrite(dt, str_replace(fname, '.txt.gz', '.methylkit.gz'), sep="\t") | |
| } | |
| convert_data_format(control_fname) | |
| convert_data_format(case_fname) | |
| file.list <- list(case_fname, control_fname) | |
| file.list <- as.list(str_replace(file.list, '.txt.gz', '.methylkit.gz')) | |
| myobj <- methRead(file.list, | |
| sample.id=list("case1", "control1"), | |
| assembly="hg38", treatment=c(1, 0), | |
| context="CpG", mincov = 10, | |
| pipeline=list(fraction = TRUE, chr.col = 1, start.col = 2, | |
| end.col = 3, coverage.col = 12, freqC.col = 7, strand.col = 13) | |
| ) | |
| meth <- unite(myobj, destrand=FALSE, min.per.group=1L) | |
| myDiff <- calculateDiffMeth(meth, mc.cores = mc_cores) | |
| # get hyper methylated bases | |
| myDiffHyper <- getMethylDiff(myDiff, qvalue=0.01, type="hyper") | |
| # get hypo methylated bases | |
| myDiffHypo <- getMethylDiff(myDiff, qvalue=0.01, type="hypo") | |
| # get all differentially methylated bases | |
| myDiffAll <- getMethylDiff(myDiff, qvalue=0.01) | |
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