Hello Bioconductors,

I am trying to annotate peaks derived with MACS and run into some errors. I hope someone can help me to get rid of these errors. I use ChIPpeakAnno and have ensembl data, but I get errors about the style. Here my R code:

> library(ChIPpeakAnno)
> library(GenomicFeatures)
>
> bed <- read.table("new.txt",sep = "\t" )
> colnames(bed)<-c("chr", "start", "end", "x")
> gr1 <- toGRanges(bed, format="BED", header=T)
duplicated or NA names found. Rename all the names by numbers.
> gr1
GRanges object with 69388 ranges and 1 metadata column:
         seqnames                 ranges strand |               x
            <Rle>              <IRanges>  <Rle> |        <factor>
  X00001       1  [ 39845630,  39845896]      * |   All_peak_1450
  X00002       1  [191889009, 191889559]      * |   All_peak_5137
  X00003       1  [212860802, 212861026]      * |   All_peak_5820
  X00004       1  [ 36306817,  36307312]      * |   All_peak_1337
  X00005       1  [ 44433306,  44433488]      * |   All_peak_1630
     ...      ...                    ...    ... .             ...
  X69384       Y    [56847145, 56847269]      * |  All_peak_69384
  X69385       Y    [56850752, 56850897]      * |  All_peak_69385
  X69386       Y    [56858855, 56858947]      * |  All_peak_69386
  X69387       Y    [56859031, 56859116]      * |  All_peak_69387
  X69388       Y    [56861359, 56861446]      * |  All_peak_69388
  -------
  seqinfo: 127 sequences from an unspecified genome; no seqlengths

> library(EnsDb.Hsapiens.v79)
> annoData <- toGRanges(EnsDb.Hsapiens.v79)
> seqlevelsStyle(annoData) <- "Ensembl"
> seqlevelsStyle(gr1) <- seqlevelsStyle(annoData)
Error in .replace_seqlevels_style(x_seqlevels, value) :
  found no sequence renaming map compatible with seqname style "NCBI" for this object
In addition: Warning message:
In `seqlevelsStyle<-`(`*tmp*`, value = c("NCBI", "Ensembl")) :
  more than one seqlevels style supplied, using the 1st one only
> annoPeaks(gr1, annoData)
Error in seqlevelsStyle(seqlevels(x)) :
  The style does not have a compatible entry for the species supported by
  Seqname. Please see genomeStyles() for supported species/style

Hope someone understands what's going on. Thanks in advance!

Regards, Ben

Ben,

The following code should work.
library(EnsDb.Hsapiens.v79)
annoData <- toGRanges(EnsDb.Hsapiens.v79)

seqlevelsStyle(gr1) <- "UCSC"

seqlevelsStyle(annoData)
#[1] "UCSC"

seqlevelsStyle(gr1)

#[1] "UCSC"

If you would prefer Ensembl seqlevelsStyle, please try the following code

seqlevelsStyle(annoData) <- "Ensembl"

seqlevelsStyle(gr1) <- "Ensembl"

Best,

Julie