bedtoGranges() error

[lowerlee]

Hi, I'm trying to download the 2018 ReMap catalogue using the code provided in the github page.

Create a local directory

demo.dir <- "~/ReMapEnrich_demo"
dir.create(demo.dir, showWarnings = FALSE, recursive = TRUE)

Use the function DowloadRemapCatalog

remapCatalog2018hg38 <- downloadRemapCatalog(demo.dir)

Load the ReMap catalogue and convert it to Genomic Ranges

remapCatalog <- bedToGranges(remapCatalog2018hg38)

I have copied and pasted the code and haven't changed any of it, but I'm getting an error when I run the bedtoGranges function:

Error in names(x) <- value :
'names' attribute [1] must be the same length as the vector [0]
In addition: Warning message:
In data.table::fread(path, header = FALSE, sep = "\t", stringsAsFactors = FALSE, :
File '~/ReMapEnrich_demo/remap2018_nr_macs2_hg38_v1_2.bed' has size 0. Returning a NULL data.table.

[CatherineBaugher]

Hey @lowerlee I had this same issue. What I think fixed it for me (or at least stopped this error message from popping) was copy-and-pasting the code from the pull request #16

A caveat here is that the results from running the enrichment on the demo data after doing this seem to be different from the enrichment plot shown in the readme tutorial (the image I generated is shown below, compare to the image on the readme where NANOG is at the top). I'm not sure why this is. I thought maybe changes to the catalog may have led to changes in the results, but the differences seem quite dramatic. It's also possible I'm doing something wrong as well, but, to my credit, I'd also like to say that I did several ReMapEnrich analyses of separate ChIP-Seq data after this and the results in all cases were very consistent with what one would expect from the experiments done. I think it's just this demo, ironically, that I can't get working properly.