使用Signac R包关联Peak与基因时遇报错求助

我正在遵循Stuart Lab的联合RNA与ATAC多组学教程，处理10X Genomics Cellranger ARC流程的输出结果。在执行「Peak与基因关联」环节时，运行LinkPeaks函数持续报错，无法生成关联结果，求解决方案。

操作流程与报错信息 #

1. RegionStats步骤（已解决警告） #

切换至ATAC assay并运行RegionStats时，最初出现seqlevels不匹配的警告：

# 切换到ATAC assay
DefaultAssay(liftoff_1_MI5_V1_SO) <- "ATAC"

# 计算每个Peak的GC含量（运行成功但有警告）
liftoff_1_MI5_V1_SO <- RegionStats(liftoff_1_MI5_V1_SO, genome = BSgenome.Mfascicularis.NCBI.5.0)
# 警告信息：Not all seqlevels present in supplied genome

通过修改BSgenome的seqlevel格式为UCSC解决了该警告：

# 修改seqlevel格式
seqlevelsStyle(BSgenome.Mfascicularis.NCBI.5.0) <- "UCSC"

# 检查修改后的seqlevels
seqlevels(BSgenome.Mfascicularis.NCBI.5.0)
# 输出示例：
# [1] "chr1"                      "chr2"                      "chr3"                      "chr4"                      "chr5"                      "chr6
# [997] "chrUn_AQIA01074376"        "chrUn_AQIA01074377"        "chrUn_AQIA01074378"        "chrUn_AQIA01074379"       
# [ reached getOption("max.print") -- omitted 6601 entries ]

# 重新切换到ATAC assay
DefaultAssay(liftoff_1_MI5_V1_SO) <- "ATAC"

# 重新运行RegionStats（无警告）
liftoff_1_MI5_V1_SO <- RegionStats(liftoff_1_MI5_V1_SO, genome = BSgenome.Mfascicularis.NCBI.5.0)

2. LinkPeaks函数持续报错 #

无论指定特定基因（如OSTN、FOS）、单个基因还是不指定基因，运行LinkPeaks均报错：

liftoff_1_MI5_V1_SO <- LinkPeaks(
  object = liftoff_1_MI5_V1_SO,
  peak.assay = "ATAC",
  expression.assay = "SCT",
  genes.use = c("OSTN", "FOS")
)

报错信息：

Processed 35548 groups out of 35548. 100% done. Time elapsed: 3s. ETA: 0s.
Testing 1 genes and 210517 peaks
  |                                                  | 0 % ~calculating  Warning: Requested more features than present in supplied data.
            Returning 0 featuresError in density.default(x = query.feature[[featmatch]], kernel = "gaussian",  :
argument 'x' must be numeric

已确认：

• 目标基因存在于SCT assay中
• ATAC assay的Peak标识符格式正常

但问题仍未解决。

内容的提问来源于stack exchange，提问作者Gen B