rcavalcante / dmrcate Goto Github PK

Dear Pete, Thanks for DMRcate tool. It has been very helpful. I really like DMP.plt function, its visualization is beautiful. But I do have couple to issues, It would be great if you can help me with these.

1. It is retuning an error for plotting a dmr no : 11376. Which is one of the DMR on my interest of the gene.

see ?DMRcatedata and browseVignettes('DMRcatedata') for documentation loading from cache Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)

It is working on the other DMRs though.

2. Is there way to print DMR (purple) completely with the DMR no. It prints half and rest get cut which does not look good.

Thanks so much for your time,
Priya

Hi there,

We have a longitudinal study where plasma sample from mice at multiple age were subjected to Illumina Methylation array. In this case, we would like to identify differential methylated CpGs (DMCs) that globally changed over the time-course, hence, we used limma time-course analysis with the intra-block correlation based block on mouse ID. We then would like to identify DMRs using dmrcate function. However, I found that the time course analysis was not a case included in the function. I understand the idea of the DMRs identification is to identify genomic regions where DMCs enriched in. Any suggestion on how I can modify the functions within the package to achieve this, especially how to indicate mice methylation array data and time-course analysis (limma)? Thank you in advance.

Best

My goal: I am trying to use DMRcate to find some differentially methylated regions.

Issue Description: When I run the following code it does not give the expected result even when I try localHub = TRUE or localHub = FALSE it still gives and error:

Attempt 1:

# Converting DMR list
results.ranges <- extractRanges(dmrcoutput, genome = "hg19")

The error is below:

Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead

Using 'localHub=TRUE'
If offline, please also see BiocManager vignette section on offline use

snapshotDate(): 2023-01-30

Error: File not previously downloaded.
Run with 'localHub=FALSE'
Traceback:

1. extractRanges(dmrcoutput, genome = "hg19")
2. eh[["EH3132"]]
3. eh[["EH3132"]]
4. .local(x, i, j = j, ...)
5. stop("File not previously downloaded.\n", " Run with 'localHub=FALSE'",
   . call. = FALSE)

Attempt 2 (with localHub = TRUE):

# Converting DMR list
results.ranges <- extractRanges(dmrcoutput, genome = "hg19", localHub=TRUE)

It gives the error:

Error in extractRanges(dmrcoutput, genome = "hg19", localHub = TRUE): unused argument (localHub = TRUE)
Traceback:

Attempt 3 (with localHub = FALSE):

# Converting DMR list
results.ranges <- extractRanges(dmrcoutput, genome = "hg19", localHub=FALSE)

It gives the error:

Error in extractRanges(dmrcoutput, genome = "hg19", localHub = FALSE): unused argument (localHub = FALSE)
Traceback:

This seems to be associated with what I believe might be an issue with the DMRcate software itself. Is there a way around this?