Question: errotr in genome infodb
0
gravatar for praveenhcu131
2.4 years ago by
praveenhcu1310 wrote:

> allRes <- lapply(chrs, workOnChr)
Working on chr1
Error in GenomeInfoDb:::getDanglingSeqlevels(x, new2old = new2old, force = force,  : 
  The following seqlevels are to be dropped but are currently in use (i.e. have ranges on them): chr2, chr3, chr4, chr5, chr6, chr7, chr8,
  chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY. Please use the 'pruning.mode'
  argument to control how to prune 'x', that is, how to remove the ranges in 'x' that are on these sequences. For example, do something like:
  
  seqlevels(x, pruning.mode="coarse") <- new_seqlevels
  
  or
  
  keepSeqlevels(x, new_seqlevels, pruning.mode="coarse")
  
  See ?seqinfo for a description of the pruning modes.

 

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by praveenhcu1310

What's the question?

What's workOnChr?

What's your sessionInfo()?

Please read our posting guide for how to properly use our support site.

Thanks,

H.

ADD REPLYlink written 2.4 years ago by Hervé Pagès ♦♦ 14k
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