plyranges.R

suppressPackageStartupMessages(library(plyranges))
suppressPackageStartupMessages(library(AnnotationHub))
suppressPackageStartupMessages(library(TxDb.Hsapiens.UCSC.hg19.knownGene))

ah <- AnnotationHub()
query(ah, c("K562","CTCF","unipk"))
peaks <- ah[["AH22543"]]
peaks <- peaks %>% keepStandardChromosomes(pruning.mode="coarse")

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
g <- genes(txdb) %>% keepStandardChromosomes(pruning.mode="coarse")
pro <- g %>% flank(width=2000,both=TRUE)

peaks <- peaks %>% mutate(promoter=overlapsAny(.,pro))

peaks %>% filter(score==1000) %>%
  group_by(promoter) %>%
  summarize(signal=mean(signalValue),
            signal.sd=sd(signalValue))