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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
MIT License
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Issues with addMotifAnnotations function in section 12.1 #277

Closed arh223 closed 3 years ago

arh223 commented 4 years ago

Hello,

I am having issues with the addMotifAnnotations function in section 12.1. I have tried running it on the sample dataset as well as my dataset, but I'm getting the same error. See below:

snATAC <- addMotifAnnotations(ArchRProj = snATAC, motifSet = "cisbp", name = "Motif") ArchR logging to : ArchRLogs/ArchR-addMotifAnnotations-197b6f5937e2-Date-2020-08-10_Time-19-58-58.log If there is an issue, please report to github with logFile! 2020-08-10 19:58:58 : Gettting Motif Set, Species : Homo sapiens, 0.002 mins elapsed. Using version 2 motifs! 2020-08-10 19:59:00 : Finding Motif Positions with motifmatchr!, 0.027 mins elapsed. Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘matchMotifs’ for signature ‘"PWMatrixList", "NULL"’

I tried removing and reinstalling all of the packages, including motifmatchr. It seems like there is some issue with how ArchR is calling a function from that package.

Also, I have attached the log file from my dataset and from the tutorial dataset.

Thank you, Alyssa

ArchR-addMotifAnnotations-15a1695ed66-Date-2020-08-10_Time-19-38-40.log ArchR-addMotifAnnotations-15fd686730f5-Date-2020-08-10_Time-19-50-02.log

cschmidl commented 4 years ago

Exact same for me! Thanks for your help!

Sophiesze commented 4 years ago

@arh223 @cschmidl Hi, I also run into this problem. Have you solved this issue yet? Would it be possible to let me know how to fix this problem? Thank you so much！

jgranja24 commented 3 years ago

Im looking into it right now.

Sophiesze commented 3 years ago

@jgranja24

Hi, would you mind tell me that if there are any updates on this issue? Thanks!

arh223 commented 3 years ago

@Sophiesze I left it for a few weeks and it managed to fix itself

rojinsafavi commented 3 years ago

I am having this error for the 10X multiomics dataset, anyone knows why it's happening?

Chris1221 commented 3 years ago

Ditto.

ArchR-addMotifAnnotations-3cdd2ef55e63-Date-2020-12-03_Time-15-23-37.log

jgranja24 commented 3 years ago

Are you sure you have a peakset added? If you run getPeakSet do you see anything returned?

This works normal for me with the test project

#Get Test Project
library(ArchR)

#Get Test Project
proj <- getTestProject()

#Add Motif Annotations
addMotifAnnotations(proj, motifSet = "cisbp", name = "Test")

> addMotifAnnotations(proj, motifSet = "cisbp", name = "Test")
ArchR logging to : ArchRLogs/ArchR-addMotifAnnotations-91bf46e714f9-Date-2020-12-12_Time-14-26-19.log
If there is an issue, please report to github with logFile!
2020-12-12 14:26:21 : Gettting Motif Set, Species : Homo sapiens, 0.001 mins elapsed.
Using version 2 motifs!
2020-12-12 14:26:23 : Finding Motif Positions with motifmatchr!, 0.03 mins elapsed.
2020-12-12 14:27:08 : Creating Motif Overlap Matrix, 0.788 mins elapsed.
2020-12-12 14:27:09 : Finished Getting Motif Info!, 0.795 mins elapsed.
ArchR logging successful to : ArchRLogs/ArchR-addMotifAnnotations-91bf46e714f9-Date-2020-12-12_Time-14-26-19.log

           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|

class: ArchRProject 
outputDirectory: /Users/jeffreygranja/Desktop/PBMCSmall 
samples(1): PBMCSmall
sampleColData names(1): ArrowFiles
cellColData names(18): Sample TSSEnrichment ... ReadsInPeaks FRIP
numberOfCells(1): 2217
medianTSS(1): 12.277
medianFrags(1): 593
rcorces commented 3 years ago

Closing due to inactivity. Feel free to comment again here and I will re-open if you still need help.