Proper formating of object to run RegionStats and LinkPeaks

[sylestiel]

Hi Tim,

When I query head(Fragments(merged)[[1]])
and head(Annotations(merged) I get the following output:

head(Fragments(merged)[[1]])
chrom start end barcode readCount
1 1 642 706 CAGAATCTCATCACTT-1 2
2 1 657 1218 CCCTCACCAGCAACCT-1 1
3 1 678 719 AGTGATGAGATAGACG-1 2
4 1 878 1027 AAAGGCTCAGAACCGA-1 2
5 1 913 1029 GGTACTTAGGCGAATA-1 2
6 1 928 1023 CCGGTAGGTAATAGCT-1 1
head(Annotation(merged))
GRanges object with 6 ranges and 5 metadata columns:
seqnames ranges strand | tx_id gene_name gene_id gene_biotype
|
ENSMMUE00000227422 1 8231-10763 - | ENSMMUT00000032773 ENSMMUG00000023296 protein_coding
ENSMMUE00000287658 1 13491-13554 - | ENSMMUT00000032773 ENSMMUG00000023296 protein_coding
ENSMMUE00000287659 1 26570-26653 - | ENSMMUT00000032773 ENSMMUG00000023296 protein_coding
ENSMMUE00000519681 1 71582-71755 + | ENSMMUT00000000911 ZNF692 ENSMMUG00000000634 protein_coding
ENSMMUE00000528194 1 72369-72558 + | ENSMMUT00000000911 ZNF692 ENSMMUG00000000634 protein_coding
ENSMMUE00000528194 1 72369-72558 + | ENSMMUT00000094839 ZNF692 ENSMMUG00000000634 protein_coding
type

ENSMMUE00000227422 exon
ENSMMUE00000287658 exon
ENSMMUE00000287659 exon
ENSMMUE00000519681 exon
ENSMMUE00000528194 exon
ENSMMUE00000528194 exon

---

seqinfo: 23 sequences (1 circular) from Mmul_10 genome

How can I modify my object (merged) to successfully run RegionStats() and LinkPeaks() functions against the BSgenome.Mmulatta.UCSC.rheMac10

The current seqlevelsStyle(merged) is 'NCBI'

I used the following to obtain the gene annotation at the start:

dbFile <- ensDbFromAH(ah["AH110914"])
edb <- EnsDb(dbFile)
annotations <- GetGRangesFromEnsDb(ensdb = edb)
genome(annotations) <- "Mmul_10"

I want to be able to introduce the chr prefix into the fragment itself. I've tried seqlevels and seqlevelsStyle using
merged@assays$ATAC@ranges@seqnames@values <- paste0("chr", merged@assays$ATAC@ranges@seqnames@values)
merged@assays$ATAC@ranges@seqnames@values <- factor(merged@assays$ATAC@ranges@seqnames@values)

merged@assays$ATAC@annotation@seqnames@values <- paste0("chr", merged@assays$ATAC@annotation@seqnames@values)
merged@assays$ATAC@annotation@seqnames@values <- factor(merged@assays$ATAC@annotation@seqnames@values)

However, I don't know how to do the same for the fragments themselves.
Can you please help with addressing this issue.

Many thanks!