Unable to link peaks to genes for multiomics data

Question

[sribas.chowdhury888]

Hello all! I am analysing a set of scMultiome data generated in our lab. I am trying to link peaks to corresponding genes using Signac's official vignette. Here is the code I used:

 library(BSgenome.Drerio.UCSC.danRer11)
    seqlevelsStyle(Control.data) <- UCSC
    Control.data <- RegionStats(Control.data, genome = BSgenome.Drerio.UCSC.danRer11)
    Control.data <- LinkPeaks(Control.data, peak.assay = 'ATAC', expression.assay = 'SCT', pvalue_cutoff = 1, score_cutoff = 0, method = 'spearman')

However, when I am running LinkPeaks, I am encountering the following error:

Control.data <- LinkPeaks(Control.data, peak.assay = 'ATAC', expression.assay = 'SCT', pvalue_cutoff = 1, score_cutoff = 0, method = 'spearman')
Testing 13975 genes and 134555 peaks
Found gene coordinates for 13500 genes
  |                                                  | 0 % ~calculating  Error in density.default(x = query.feature[[featmatch]], kernel = "gaussian",  : 
  argument 'x' must be numeric
In addition: 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': KN147632.2, KN147636.1, KN147637.2, KN147651.2, KN149685.1, KN149686.1, KN149688.2, KN149689.2, KN149690.1, KN149696.2, KN149702.1, KN149707.2, KN149710.1, KN149711.1, KN149713.1, KN149725.1, KN149729.1, KN149732.1, KN149735.1, KN149739.1, KN149749.1, KN149764.1, KN149778.1, KN149779.1, KN149782.1, KN149790.1, KN149793.1, KN149797.1, KN149800.1, KN149813.1, KN149816.1, KN149818.1, KN149840.1, KN149847.1, KN149855.1, KN149857.1, KN149859.1, KN149874.1, KN149880.1, KN149883.1, KN149884.1, KN149895.1, KN149909.1, KN149912.1, KN149932.1, KN149943.1, KN149946.1, KN149948.1, KN149955.1, KN149959.1, KN149968.1, KN149978.1, KN149984.1, KN149992.1, KN149995.1, KN149997.1, KN149998.1, KN150000.1, KN150008.1, KN150015.1, KN150019.2, KN150030.1, KN150032.1, KN150041.2, KN150062.1, KN150067.1, KN150086.1, KN150098.1, KN150102.1, KN150104.1, KN150115.1, KN150120.1, KN150125.1, KN150131.1, KN150137.1, KN150141.1, KN15015 [... truncated]
2: In MatchRegionStats(meta.feature = meta.use, query.feature = pk.use[x,  :
  Requested more features than present in supplied data.
            Returning 0 features

From what I read, this usually arises when there is a naming mismatch between data and genome. However that is not the case with my data as I checked here:

> seqlevelsStyle(Control.data)
[1] "UCSC"
> seqlevelsStyle(BSgenome.Drerio.UCSC.danRer11)
[1] "UCSC"

So, I am now confused as to how to solve this. Can anyone please help me out on how to resolve this?