Entering edit mode
I was testing following the Motif analysis vignette (https://satijalab.org/signac/articles/mouse_brain_vignette.html), and i have build around it some code and it was working good till yesterday. Today, I start got error when running the following couple lines
annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Mmusculus.v79)
seqlevelsStyle(annotations) <- 'UCSC'
Then i get the following error message
Error in .order_seqlevels(chrom_sizes[, "chrom"]) :
!anyNA(m31) is not TRUE
17.stop(simpleError(msg, call = if (p <- sys.parent(1L)) sys.call(p)))
16.stopifnot(!anyNA(m31)) at mm10.R#24
15..order_seqlevels(chrom_sizes[, "chrom"]) at mm10.R#42
14.GET_CHROM_SIZES(goldenPath.url = goldenPath.url)
13..get_chrom_info_for_registered_UCSC_genome(script_path, assembled.molecules.only = assembled.molecules.only,
map.NCBI = map.NCBI, add.ensembl.col = add.ensembl.col, goldenPath.url = goldenPath.url,
recache = recache)
12.getChromInfoFromUCSC(new_genome, map.NCBI = TRUE)
11.(function (seqlevels, genome, new_style)
{
ans <- DataFrame(seqlevels = seqlevels, genome = genome)
if (is.na(genome) || !(new_style %in% c("NCBI", "RefSeq", ...
10.mapply(FUN = FUN, ..., MoreArgs = MoreArgs, SIMPLIFY = SIMPLIFY,
USE.NAMES = USE.NAMES)
9.eval(mc, env)
8.eval(mc, env)
7.eval(mc, env)
6.standardGeneric("mapply")
5.mapply(.set_seqlevelsStyle_from_seqlevels_and_genome, genome2seqlevels,
names(genome2seqlevels), MoreArgs = list(value), SIMPLIFY = FALSE,
USE.NAMES = FALSE)
4.`seqlevelsStyle<-`(`*tmp*`, value = value)
3.`seqlevelsStyle<-`(`*tmp*`, value = value)
2.`seqlevelsStyle<-`(`*tmp*`, value = "UCSC")
1.`seqlevelsStyle<-`(`*tmp*`, value = "UCSC")
The error seems that i can not revert the UCSC from the EnsDb.Mmusculus.v79, and this is not the case for EnsDb.Hsapiens.v86 which works fine.
for complete reference, here is my sessionInfo()
[1] EnsDb.Mmusculus.v79_2.99.0 ensembldb_2.14.1 AnnotationFilter_1.14.0 GenomicFeatures_1.42.3 AnnotationDbi_1.52.0
[6] Biobase_2.50.0 Signac_1.2.1 GenomicRanges_1.42.0 GenomeInfoDb_1.26.7 IRanges_2.24.1
[11] S4Vectors_0.28.1 BiocGenerics_0.36.1
Any help ?
