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leekgroup / derfinder

R package for DER Finder, a method for differential expression analysis of RNA-seq data
http://biostatistics.oxfordjournals.org/content/early/2014/01/06/biostatistics.kxt053.short?rss=1
MIT License
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makeTranscriptDbFromUCSC() returns "'data' must be of a vector type" error #15

Open brianhigh opened 9 years ago

brianhigh commented 9 years ago

It looks like changes in UCSC have introduced a problem with running this beta derfinder with R 2.15.3.

In the sample code analysis_code.R:

exons = getAnnotation("hg19","knownGene")
Warning message:
In .local(.Object, ...) : NAs introduced by coercion
Error in genome(ucscCart(x)) : 
  error in evaluating the argument 'x' in selecting a method for function 'genome': Error in matrix(unlist(pairs), nrow = 2) : 
  'data' must be of a vector type

Error in getAnnotation("hg19", "knownGene") : 
  Problem accessing requested UCSC annotation - likely there is a problem with genome or tablename arguments. Use ucscGenomes() to see acceptable genomes; use supportedTables(genome) to see acceptable tablenames for your genome.

A test:

a <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "knownGene")
Warning message:
In .local(.Object, ...) : NAs introduced by coercion
Error in genome(ucscCart(x)) : 
  error in evaluating the argument 'x' in selecting a method for function 'genome': Error in matrix(unlist(pairs), nrow = 2) : 
  'data' must be of a vector type