Error when using a custom motif annotation in addMotifAnnotations()

[xmliu01]

Discussed in https://github.com/GreenleafLab/ArchR/discussions/1932

^{Originally posted by **xmliu01** April 21, 2023} Hello, I am using ArchR to analysis my single-cell ATAC-seq data in wheat, but we I using the addMotifAnnotations(), I got the bellow errors. ArchR logging to : ArchRLogs/ArchR-addMotifAnnotations-64d158ef102d-Date-2023-04-20_Time-21-49-47.log If there is an issue, please report to github with logFile! 2023-04-20 21:49:57 : Gettting Motif Set, Species : , 0.183 mins elapsed. 2023-04-20 21:49:59 : Finding Motif Positions with motifmatchr!, 0.207 mins elapsed. 2023-04-20 22:17:30 : All Motifs Overlap at least 1 peak!, 27.726 mins elapsed. 2023-04-20 22:17:30 : Creating Motif Overlap Matrix, 27.726 mins elapsed. **Error in Matrix::sparseMatrix(i = queryHits(overlapMotifs), j = match(names(allPositions), : 'i' and 'j' must not contain NA** Because there isn't a motifSet for wheat, so I provided a custom motif list using motifPWMs. I provided a custom motif set in meme format and used the read_meme() in package universalmotif to read it. And then I converted it into PWMatrix using convert_motifs() in package TFBSTools. Lastly, I used PWMatrixList() in TFBSTools package to convert PWMatrix into PWMatrixList. So, I thought the format of this custom motif set is correct. But when I run addMotifAnnotations(), I go the above error. And here is my code: `library(universalmotif)` `library(TFBSTools)` `library(chromVAR)` `library(motifmatchr)` `motif=read_meme("~/TF-motif/meme/Ath_TF_binding_motifs.meme")` `motif_all=convert_motifs(motif,class="TFBSTools-PWMatrix")` `tair.motif=do.call(PWMatrixList,motif_all)` `projSpike2=addMotifAnnotations(projSpike2,name="Motif",motifPWMs=tair.motif)` So, if anyone knows how to solve this problem. And I also attached my log file. [ArchR-addMotifAnnotations-64d158ef102d-Date-2023-04-20_Time-21-49-47.log](https://github.com/GreenleafLab/ArchR/files/11295349/ArchR-addMotifAnnotations-64d158ef102d-Date-2023-04-20_Time-21-49-47.log)

[rcorces]

Hi @xmliu01! Thanks for using ArchR! I am currently on vacation and will not be responding to any issues or discussion threads until 5/5.
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[xmliu01]

I thought I have solved this problem. I found that the names of tair.motif is NULL, and it will got the NA results. So, if I add the names to tair.motif using names(tair.motif)=ID(tair.motif), then it worked.

The complete code is

library(TFBSTools)
library(chromVAR)
library(motifmatchr)
motif=read_meme("~/TF-motif/meme/Ath_TF_binding_motifs.meme")
motif_all=convert_motifs(motif,class="TFBSTools-PWMatrix")
tair.motif=do.call(PWMatrixList,motif_all)
names(tair.motif)=ID(tair.motif)
projSpike2=addMotifAnnotations(projSpike2,name="Motif",motifPWMs=tair.motif)

And you can also download the motifSet from JASPAR using TFBSTools

library(TFBSTools)
library(JASPAR2020)
tair.motif=getMatrixSet(x=JASPAR2020,opts=list(collection="CORE",species="3702",matrixtype="PWM"))
projArchR=addMotifAnnotations(projArchR,name="Motif",motifPWMs=tair.motif,force=T)