I have asked this question on bioconductor, but I didn't get any response there. I hope I can get some help here.
I am trying to annotate peaks derived with MACS2 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
I hope that someone knows what's going on, I think that the style is not correct defined, but don't know how to correct this.
Thanks in advance.