ChIPpeakAnno: No seqlevelsStyle compatible entry
0
0
Entering edit mode
tom.dean • 0
@cc0a72b7
Last seen 10 days ago
United Kingdom

I am attempting to use ChIPpeakAnno to annotate peaks I have found from DAPseq data. I am using annotatePeakInBatch function, please see code below.

Annotated_peaks <- annotatePeakInBatch(Peaks,featureType = "TSS", PeakLocForDistance = "middle", AnnotationData = genes) 

Error in seqlevelsStyle(seqlevels) : 
  The style does not have a compatible entry for the species supported by Seqname. Please see genomeStyles() for supported species/style

In response to this error, I modified the chromosome names in seqnames using the following code.

rename_chr_Wheat = function(x) {
  renameSeqlevels(x, c("Chr1A" = "Chr1", "Chr1B" = "Chr2", "Chr1D" = "Chr3", "Chr2A" = "Chr4", "Chr2B" = "Chr5", "Chr2D" = "Chr6", "Chr3A" = "Chr7", "Chr3B" = "Chr8", "Chr3D" = "Chr9", "Chr4A" = "Chr10", "Chr4B" = "Chr11", "Chr4D" = "Chr12", "Chr5A" = "Chr13", "Chr5B" = "Chr14", "Chr5D" = "Chr15", "Chr6A" = "Chr16", "Chr6B" = "Chr17", "Chr6D" = "Chr18", "Chr7A" = "Chr19", "Chr7B" = "Chr20", "Chr7D" = "Chr21", "ChrUnknown" = "Chr22"))
}

Peaks_edited <- rename_chr_Wheat(Peaks)
genes_edited <- rename_chr_Wheat(genes)
ChIPSeqData • 49 views
ADD COMMENT

Login before adding your answer.

Traffic: 342 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6