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quadbio / scMultiome_analysis_vignette

Tutorial of single-cell RNA-ATAC multiomic sequencing data analysis
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Issue with motif analysis using JASPAR #4

Open yojetsharma opened 7 months ago

yojetsharma commented 7 months ago

I am not sure how to go ahead with the analysis. Can someone please help?

> pfm <- getMatrixSet(
+     x = JASPAR2020,
+     opts = list(collection = "CORE", tax_group = 'vertebrates', all_versions = FALSE)
+ )
> df_pfm <- data.frame(t(sapply(pfm, function(x)
+     c(id=x@ID, name=x@name, symbol=ifelse(!is.null(x@tags$symbol),x@tags$symbol,NA)))))
> 
> seurat <- AddMotifs(seurat, genome = BSgenome.Hsapiens.UCSC.hg38, pfm = pfm)
Building motif matrix
Warning in CreateMotifMatrix(features = object, pwm = pfm, genome = genome,  :
  Not all seqlevels present in supplied genome
Finding motif positions
Creating Motif object
Warning in RegionStats.default(object = regions, genome = genome, verbose = verbose,  :
  Not all seqlevels present in supplied genome
Warning messages:
1: In .merge_two_Seqinfo_objects(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270772v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr4_GL000 [... truncated]
2: In .merge_two_Seqinfo_objects(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': chrM, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270759v1_alt, chr1_KI270760v1_alt, chr1_KI270761v1_alt, chr1_KI270762v1_alt, chr1_KI270763v1_alt, chr1_KI270764v1_alt, chr1_KI270765v1_alt, chr1_KI270766v1_alt, chr1_KI270892v1_alt, chr2_GL383521v1_alt, chr2_GL383522v1_alt, chr2_GL582966v2_alt, chr2_KI270767v1_alt, chr2_KI270768v1_alt, chr2_KI270769v1_alt, chr2_KI270770v1_alt, chr2_KI270771v1_alt, chr2_KI270772v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270775v1_alt, chr2_KI270776v1_alt, chr2_KI270893v1_alt, chr2_KI270894v1_alt, chr3_GL383526v1_alt, chr3_JH636055v2_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270779v1_alt, chr3_KI270780v1_alt, chr3_KI270781v1_alt, chr3_KI270782v1_alt, chr3_KI270783v1_alt, chr3_KI270784v1_alt, chr3_KI270895v1_alt, chr3_KI270924v1_alt, chr3_KI270934v1_alt, chr3_KI270935v1_alt, chr3_KI270936v1_alt, chr3_KI270937v1_alt, chr4_GL000 [... truncated]
> open_peaks <- AccessiblePeaks(seurat)
> peaks_matched <- MatchRegionStats(meta.feature = seurat[['ATAC']]@meta.features[open_peaks, ],
+                                   query.feature = seurat[['ATAC']]@meta.features[marker_peak_ct$feature, ],
+                                   n = 50000)
Matching GC.percent distribution
Error in density.default(x = query.feature[[featmatch]], kernel = "gaussian",  : 
  'x' contains missing values