Any answers would be highly appreciated as I've been stuck on this for a while. I analyze epigenetic data and process DMR lists and I'm currently having issues producing a pie chart that shows the distribution of the repeat sequences in my samples. I've already done this for genomic distribution (TSS, 5' UTR etc.) but I can't seem to be able to figure out how I can use RepeatMasker to do the same thing.
Here's exactly what I did for the genomic distribution pie chart:
peakAnno <- annotatePeak("~/Desktop/1-m1Vsm2.bed.gz", tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Mm.eg.db") plotAnnoPie(peakAnno)
The results looked fine but then I tried the following using the UCSC RepeatMasker package in R (mm39 mouse sample). I've read the documentation and everything and still haven't figure it out. I got the following error:
#Annotate peaks (with repeat sequences) & plot ah <- AnnotationHub()query(ah, c("RepeatMasker", "Mus musculus")) rmskmm39 <- ah[["AH99013”]] peakAnnoRepeat <- annotatePeak("~/Desktop/1-m1Vsm2.bed.gz", tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="rmskmm39") plotAnnoPie(peakAnnoRepeat) Warning messages: 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘rmskmm39’ 2: In getGeneAnno(annoDb, peak.gr$geneId, type, columns) : ID type not matched, gene annotation will not be added..
I thought extracting the mm39 masked repeat track would act as the annotation track instead of "org.Mm.eg.db" as was used in the original working example. If anyone has any pointers or solutions, that'd be great.