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See #687 |
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Hello, I am trying to analysis RNA+ATAC and use Signac .
when i trying to make a annotation file , code as follows
library(EnsDb.Mmusculus.v79)
annotations <- GetGRangesFromEnsDb(ensdb =EnsDb.Mmusculus.v79 )
seqlevelsStyle(annotations) <- 'UCSC'
there is a error:
Error in .order_seqlevels(chrom_sizes[, "chrom"]) :
!anyNA(m31) is not TRUE
I find there is discuss about this error , as link: Bioconductor/GenomeInfoDb#27 (comment)
but i can not solve the error in follow-up code
chrom_assay <- CreateChromatinAssay(
counts = atac_counts,
sep = c(":", "-"),
genome = 'mm10',
fragments = frag.file,
min.cells = 10,
annotation = annotations
)
there is a error too:
Error in .order_seqlevels(chrom_sizes[, "chrom"]) :
!anyNA(m31) is not TRUE
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