hi, I have a question or suggestion for you all. I have some peaks and I would to annotate them. My goal is to extend the annotation 10000 upstream from the start of the gene and 10000 downstream from the end of the gene body. So I don’t want to set +10.000/-10000 from TSS. chipseeker seems that doesn’t allow to define the parameters like TSS or gene body start/end:
annotatePeak {ChIPseeker}
Usage
annotatePeak(
peak,
tssRegion = c(-3000, 3000),
TxDb = NULL,
level = "transcript",
assignGenomicAnnotation = TRUE,
genomicAnnotationPriority = c("Promoter", "5UTR", "3UTR", "Exon", "Intron",
"Downstream", "Intergenic"),
annoDb = NULL,
addFlankGeneInfo = FALSE,
flankDistance = 5000,
sameStrand = FALSE,
ignoreOverlap = FALSE,
ignoreUpstream = FALSE,
ignoreDownstream = FALSE,
overlap = "TSS",
verbose = TRUE
)
On the other hand, maybe I could use chippeakanno, that has this option:
annoPeaks {ChIPpeakAnno}
Description
Annotate peaks by annoGR object in the given range.
Usage
annoPeaks(
peaks,
annoData,
bindingType = c("nearestBiDirectionalPromoters", "startSite", "endSite", "fullRange"),
bindingRegion = c(-5000, 5000),
ignore.peak.strand = TRUE,
select = c("all", "bestOne"),
...
)
setting
bindingType = "fullRange",
bindingRegion = c(-10000, 10000)
However, I’ve tried both:
1) chipseeker <- annotatePeak(as(DARS_up_gr,"GRanges"),
tssRegion = c(-10000,10000),
TxDb = TxDB.mm10.ensembl, level = "gene",
annoDb = "org.Mm.eg.db"
,overlap = 'all')
2) chipepeakanno <- ChIPpeakAnno::annoPeaks(DARS_up_gr,anno_txdb , bindingType = "fullRange", bindingRegion = c(-10000,10000), select = "all")
What do you suggest? what could be the best way to do it?
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