Error in UseMethod(generic = "RunChromVAR", object = object) : no applicable method for 'RunChromVAR'

[elanur-yilmaz]

Dear Team, I am new at multiome analysis and running a tutorial (https://github.com/quadbio/scMultiome_analysis_vignette/blob/main/Tutorial.md) in my data set.

At "Step 4. ChromVAR: another motif enrichment analysis" while I was running seurat <- RunChromVAR(seurat, genome = BSgenome.Hsapiens.UCSC.hg38) in my data set, I got the error below.

Error in UseMethod(generic = "RunChromVAR", object = object) : no applicable method for 'RunChromVAR' applied to an object of class "c('Assay', 'KeyMixin')"

I restarted the session, and checked online but did not find a solution. Can anyone help me?

Thank you very much,

Elanur

[timoast]

It's hard to know what the issue is without seeing the full code, but from the error message it looks like you're trying to run this function on a standard assay rather than a chromatin assay

[elanur-yilmaz]

Dear Tim, Thank you for your response. I directly tried a code that I shared. And here how it is:

p.s. I also gas error setNames function :/

Step 4. ChromVAR: another motif enrichment analysis

BiocManager::install("chromVAR") library(chromVAR) library(BSgenome.Hsapiens.UCSC.hg38)

qc1 <- RunChromVAR(qc1, genome = BSgenome.Hsapiens.UCSC.hg38)

DefaultAssay(qc1) <- "chromvar" DA_motifs_ct <- wilcoxauc(qc1, group_by = "nwidx", seurat_assay = "chromvar") %>% mutate(symbol = setNames(ifelse(is.na(df_pfm$symbol), df_pfm$name, df_pfm$symbol), df_pfm$id)[feature])

enriched_motifs_ct <- DA_motifs_ct %>% filter(padj < 0.01 & auc > 0.7) %>% group_by(group) top_motifs_ct <- top_n(enriched_motifs_ct, 3, wt=auc)

[timoast]

it looks like you're trying to run this on the RNA assay rather than the ATAC, try changing the assay first