Error merging samples with unite()

[EMILY KERNS]

Hello!

I am trying to merge my RRBS samples using the unite() function. It worked previously for me, and I haven't changed the argument at all. I did add a normalization step prior to merging my samples, and that's when I started getting this error. Last Friday I updated R and reinstalled all of my packages, and it worked for me again. However, I went to go try to run my code again today and it's not working. Does anyone know what might be causing this error?

myobj=methRead(file.list,
               sample.id=list("SampleIDs"),
               assembly="ReferenceGenome",
               treatment=c(treatments),
               context="CpG",
               mincov = 10
)

filtered.myobj=filterByCoverage(myobj,lo.count=10,lo.perc=NULL,
                                hi.count=NULL,hi.perc=99.9)

normalized.myobj=normalizeCoverage(filtered.myobj, method="median")

meth=unite(normalized.myobj, destrand=TRUE)

Error in `unite()`: ! Arguments in `...` must be passed by position, not name. ✖ Problematic argument: • destrand = TRUE Run `rlang::last_trace()` to see where the error occurred. > rlang::last_trace() <error/rlib_error_dots_named> Error in `unite()`: ! Arguments in `...` must be passed by position, not name. ✖ Problematic argument: • destrand = TRUE --- Backtrace: ▆ 1. └─tidyr::unite(normalized.myobj, destrand = TRUE) Run rlang::last_trace(drop = FALSE) to see 4 hidden frames. > rlang::last_trace(drop = FALSE) <error/rlib_error_dots_named> Error in `unite()`: ! Arguments in `...` must be passed by position, not name. ✖ Problematic argument: • destrand = TRUE --- Backtrace: ▆ 1. └─tidyr::unite(normalized.myobj, destrand = TRUE) 2. └─rlang::check_dots_unnamed() 3. └─rlang:::action_dots(...) 4. ├─base (local) try_dots(...) 5. └─rlang (local) action(...)

Thanks!

Emily

[Alexander Blume]

Hi Emily,

This sounds very much like the methylkit+tidyverse issue (https://github.com/al2na/methylKit/issues/132), which I thought was resolved since version 1.9.1 of methylKit. 

You should be able to fix the problem by explicitly using  methylKit::unite in your code.

Best,

Alex

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[EMILY KERNS]

Hi Alex,

It worked! Thank you!

Cheers,

Emily