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tdhock / PeakSegFPOP-paper

Functional pruning optimal partioning algorithm for PeakSeg constrained segmentation model
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Missing dataset (`regions.RData` file) #2

Open nhintruong opened 2 months ago

nhintruong commented 2 months ago

I'm attempting to run the source code from https://github.com/tdhock/PeakSegFPOP-paper/blob/master/figure-large-margin.R, but I'm unable to locate the required regions.RData file in the repository.

Here is the error I met:

> set.name <- ""H3K4me3_TDH_immune""
> chunk.id <- 5
> chunk.name <- paste0(set.name, ""/"", chunk.id)
> regions.file <- file.path(""data"", set.name, chunk.id, ""regions.RData"")
> load(regions.file)
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'data/H3K4me3_TDH_immune/5/regions.RData', probable reason 'No such file or directory'"

@tdhock Could you please check if this folder is still available or if it has been renamed? Thank you for your assistance

tdhock commented 2 months ago

these data need to be downloaded from https://rcdata.nau.edu/genomic-ml/chip-seq-chunk-db/ for example https://rcdata.nau.edu/genomic-ml/chip-seq-chunk-db/data/H3K4me3_TDH_immune/5/regions.RData