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Check if methylKit::unite with min.per.group filter would work for given sample number and chunk size
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| library(methylKit) | |
| test_overflow <- function(n_samples, chunk_size) { | |
| # simulate 10 samples | |
| res <- dataSim(replicates = 10, | |
| sites = 1e3, | |
| treatment = rep(1, 10)) |> | |
| makeMethylDB(dbdir = tempdir()) |> # convert to tabix | |
| suppressMessages() |> | |
| getDBPath() |> | |
| TabixFile(yieldSize = 100) |> | |
| open() |> | |
| Rsamtools::scanTabix() |> | |
| paste(collapse = "\n") |> | |
| paste0(collapse = "\n") |> | |
| object.size() * (n_samples / 10) * (chunk_size / 100) | |
| if(res < 2^31 - 1) { | |
| message("chunk size is fine") | |
| return(invisible(TRUE)) | |
| } | |
| message( | |
| sprintf( | |
| "chunk would exceed 2^31-1 bytes by factor %2.f", | |
| as.numeric(res)/(2^31-1) | |
| ) | |
| ) | |
| message( | |
| sprintf( | |
| "Consider reducing chunk size to > %0.f", | |
| chunk_size / (as.numeric(res)/(2^31-1)) |> round() | |
| ) | |
| ) | |
| return(invisible(chunk_size / (as.numeric(res)/(2^31-1)) |> round())) | |
| } | |
| test_overflow(n_samples = 1000, chunk_size = 500000) | |
| test_overflow(n_samples = 1000, chunk_size = 50000) | |
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