Problem with annotations using annotatr
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@6694d8c3
Last seen 9 days ago
United States

Hi, I am having issues creating the annotations GRrange for annotatr. It keeps showing the same error. I tried the trim option bu nothing happened, I updated R, Rstudio, Bioconductor and restart everything and nothing. The code run without any issue in a different computer. Could someone help me solving this issue?

Code should be placed in three backticks as shown below

extraCols = c(diff_meth = 'character', mu0 = 'numeric', mu1 = 'numeric')
dm_regions = read_regions(con = 'wholemann_annot.bed', genome = 'mm10', extraCols = extraCols, format = 'bed')
annots = c('mm10_cpgs','mm10_basicgenes','mm10_genes_intergenic','mm10_genes_intronexonboundaries','mm10_genes_promoters','mm10_genes_introns','mm10_genes_exons')

annotations = build_annotations(genome = 'mm10', annotations = annots)

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
> extraCols = c(diff_meth = 'character', mu0 = 'numeric', mu1 = 'numeric')
> dm_regions = read_regions(con = 'wholemann_annot.bed', genome = 'mm10', extraCols = extraCols, format = 'bed')
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

> annots = c('mm10_cpgs','mm10_basicgenes','mm10_genes_intergenic','mm10_genes_intronexonboundaries','mm10_genes_promoters','mm10_genes_introns','mm10_genes_exons')
> annotations = build_annotations(genome = 'mm10', annotations = annots)
'select()' returned 1:1 mapping between keys and columns
Building promoters...
Building 1to5kb upstream of TSS...
Building intergenic...
Building 5UTRs...
Building 3UTRs...
Building exons...
Building introns...
Building intron exon boundaries...
Building CpG islands...
Building CpG shores...                                                                                                                                            
Building CpG shelves...
Building inter-CpG-islands...
Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 2 out-of-bound ranges located on sequence chr4_JH584295_random. Note that ranges located on a sequence whose length is
  unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags
  of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information.
annotatr • 70 views
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Entering edit mode
@6694d8c3
Last seen 9 days ago
United States

Problem was solved

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