error in duplicate row.names in getting gene symbols

Question

[Kai_Qi]

Hi:

I am running RNA-seq analysis. I met an error in the step of extraction features and map symbols to genes. My running code is:

library(GenomicFeatures)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
TxDb <- TxDb.Mmusculus.UCSC.mm10.knownGene
library(ASpli)
features <- binGenome(TxDb)
symbols <- data.frame(row.names = genes(TxDb),
                      symbol = paste(genes(TxDb)))*

the occurring error is:

symbols <- data.frame(row.names = genes(TxDb),
+                       symbol = paste(genes(TxDb)))
Error in data.frame(row.names = genes(TxDb), symbol = paste(genes(TxDb))) : 
  duplicate row.names: chr4:61224307-61674094:-, chr17:34145416-34160229:+, chr9:44101770-44109187:+, chr1:133309823-133329722:+, chr1:88103257-88220002:+

What should I correct?

Cai

[Kai_Qi]

Hi Guys:

I am sorry to have so many errors. When I put the command : "features <- binGenome (TxDb, geneSymbols = symbols)", I got an error like this:

Error in features < binGenome(TxDb, geneSymbols = symbols) : 
  comparison (3) is possible only for atomic and list types
In addition: Warning messages:
1: In normSplitFactor(f, x) :
  'NROW(x)' is not a multiple of split factor length
2: In normSplitFactor(f, x) :
  'NROW(x)' is not a multiple of split factor length

What does that mean?

Thank you,

Cai

Answer 1

[shawn.w.foley]

A data frame in R requires unique row.names, a simple work around would be to make a data frame with an additional column and no row names:

symbols <- data.frame(genes = genes(TxDb), symbol = paste(genes(TxDb)))

[Kai_Qi]

Thanks Shawn, I put the command in the script it did not pop out error. Thanks a lot for your help

[Ram]

^ This is the way to go. Plus, remember that row names are not an ideal feature of data.frames, you should prefer columns whenever possible. row.names makes sense in matrices, not in data frames.

[ATpoint]

While this is technically a solution, it is still an issue that there are duplicated gene names /ranges. Can you try and update the package to the newest version? On my machine, downloaded the package just yet, the code runs without errors. Also the ranges for one of these genes is different, e.g. your chr4:61224307-61674094:- is in my results chr4:61224307-61228286:-. Maybe you have a very old version?