warning trying to create a TxDB for S.pombe
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1
Entering edit mode
4.6 years ago
Lila M ★ 1.1k

Hi! I want to annotate the genes with a peak for a S.pombe ChiPseq experiment. I always do that using ChIPseeker. As there is no TxDB genome for S.pombe, I've created it as follow

txdb_pombe <- makeTxDbFromGFF("Schizosaccharomyces_pombe.ASM294v2.34.gff3.gz", format="gff3", organism = "Schizosaccharomyces pombe", taxonomyId = "4896")

But I have the follow warning:

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: Named parameters not used in query: internal_chrom_id, chrom, length, is_circular 
2: Named parameters not used in query: internal_id, name, type, chrom, strand, start, end 
3: Named parameters not used in query: internal_id, name, chrom, strand, start, end 
4: Named parameters not used in query: internal_id, name, chrom, strand, start, end 
5: Named parameters not used in query: internal_tx_id, exon_rank, internal_exon_id, internal_cds_id 
6: Named parameters not used in query: gene_id, internal_tx_id

And when I've tried to run the program

for (i in fileList){
   peak <- readPeakFile(i, header=F)
  peakAnno <- annotatePeak(peak, tssRegion=c(-500, 2000), TxDb= "txdb_pombe")
  print(peakAnno)
    write.table(peakAnno, paste("annot_", i, sep="") , sep="\t", col.names=T, row.names = F, quote=F)
}

The follow error is reported

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘metadata’ for signature ‘"character"’

Any suggestion?

Many thanks!

ChIPseeker pombe TxDB GRanges Metadata • 1.8k views
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2
Entering edit mode
4.6 years ago
ddiez ★ 1.9k

The help for annotatePeak says this about the TxDb argument:

TxDb TxDb object

But you are passing a character string "txdb_pombe". Try this instead:

annotatePeak(peak, tssRegion = c(-500, 2000), TxDb = txdb_pombe)
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Entering edit mode

Totally right, problem solved!!!

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