Fix issues processing chromatin assay and genome annotation in scMultiome data (Signac)

[randomForest97]

Fix issues processing chromatin assay and genome annotation in scMultiome data

I tried to use the package for scMultiome data and ran into several issues when processing the chromatin assay from Signac:

1. The chromatin assay had a different name than "peaks". I added the option to specify the chromatin assay name explicitly.

2. The code accessed the genome annotation via obj@assays[["peaks"]]@annotation@seqinfo@genome[1], but if this value does not match "hg19", "hg38", "mm10" or "mm9", the corresponding GTF file was not copied. My data used "GRCm38", which caused the problem.

3. The GenomicRanges package was not loaded, causing an error when creating GRanges objects, for example here:

chromSizes <- GRanges(
  seqnames = availableChr,
  ranges = IRanges(
    start = rep(1, length(x = availableChr)),
    end = as.numeric(x = chromLengths)
  )
)

4. The annotation information was accessed via obj@assays[[chrom_assay_name]]@seqinfo, but in my case it was stored under obj@assays[[chrom_assay_name]]@annotation@seqinfo. I adapted the code to check both locations.