ChIPSeeker

library(ChIPseeker)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
library(org.Mm.eg.db)
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene

cbf = readPeakFile ("MACS2_bdgdiff_Peaks_CBF_H3K27me3.bed")
peakAnno_cbf = annotatePeak(cbf, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Mm.eg.db")
cbf_anno = as.data.frame (peakAnno_cbf, row.names= NULL, optional = FALSE)
write.csv(cbf_anno, file ="MACS2_bdgdiff_Peaks_CBF_H3K27me3.bed.anno.csv")