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plevritis-lab / remi

The REMI package is written in R and is designed to predict ligand receptor interactions within a microenvironment given RNA-sequencing data. It regularizes communities of ligand and receptors that have a high probability of being transcriptionally linked.
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Bulk RNA example: remi.obj <- remi(data.obj) error #2

Open cdkodira opened 1 year ago

cdkodira commented 1 year ago

In the bulk RNA example, when I run the following code remi.obj <- remi(data.obj) I get this error: Detecting communitiesError in if (unique(commnums) == unique(communities)) { : the condition has length > 1

smeiersab commented 1 year ago

Hi, I came across the same error. It's caused by an error in the function clusterLouvain (script load_subfunctions.R), where twice the condition can have length >1 (line 119 and 128). Adaptingif(unique(commnums) == unique(communities)) to if(all(unique(commnums) == unique(communities))) and suppressWarnings(if(is.na(final.comms)) to suppressWarnings(if(all(is.na(final.comms))) worked for me.

cdkodira commented 1 year ago

Unfortunately, it did not fix the problem for me. Do you have any plans for updating the code the with fix? Thanks,

smeiersab commented 1 year ago

ah, sorry it didn't work for you. I'm not part of the REMI team, so can't help you with that

ayu1 commented 1 year ago

Hi,

I can take a look next week.

Best, Alice

On Mon, Jun 12, 2023 at 6:14 PM cdkodira @.***> wrote:

Unfortunately, it did not fix the problem for me. Do you have any plans for updating the code the with fix? Thanks,

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