add_nearest_distance not working

tidyomics / plyranges

A grammar of genomic data transformation

https://tidyomics.github.io/plyranges/

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add_nearest_distance not working #93

Closed u2058152 closed 3 years ago

u2058152 commented 3 years ago

I installed plyranges and carried out the library command. I get an error saying add_nearest_distance command is not found.

Command executed:

peaks_annotated <- genes %>%

add_nearest_distance(peaks) %>%

join_overlap_inner(peaks, maxgap = 3000)

Error found: Error in add_nearest_distance(., peaks) : could not find function "add_nearest_distance"

snystrom commented 3 years ago

Hey, I can't reproduce this on my end. Would you mind trying a couple things?

First, could you post the output of SessionInfo()?
Can you confirm genes and peaks are GRanges objects: class(genes) and class(peaks)?
Can you call the function with :: like so plyranges::add_nearest_distance(genes, peaks)?
Finally, do other plyranges functions work in this session (ie mutate(genes, example = "test")? I would try restarting & reloading to see if that resolves the issue.

u2058152 commented 3 years ago

I installed a newer version of R (I was using R 4.0.2) and add_nearest_distance now works. However, when I try to knit an r markdown file I get the following error message:

snystrom commented 3 years ago

This sounds like a namespacing issue. In the Rmd you're calling library(plyranges) right? If you switch your call to plyranges::add_nearest_distance does that fix it?

u2058152 commented 3 years ago

Thanks for your help this resolves the problem.