238    ◾    Bioinformatics

#get the NCBI Entrez IDs

entrez1 <- chip1_annot$geneId

# Obtain the gene symbols for the set of Entrez IDs from the

database

annotations_edb1 <- AnnotationDbi::select(EnsDb.Hsapiens.v75,

keys = entrez1,

columns = c(“GENENAME”),

keytype = “ENTREZID”)

#Convert IDs to character type to merge

annotations_edb1$ENTREZID

<- as.character(annotations_edb1$ENTREZID)

# Write Chip1 annotation to file

chip1_annot %>% left_join(annotations_edb1,

by=c(“geneId”=”ENTREZID”)) %>%

write.table(file=”Chip1_peak_annotation.txt”,

sep=”\t”, quote=F, row.names=F)

# Write Chip2 annotation to a file

chip2_annot <- data.frame(annotated_peaks[[“chip2”]]@anno)

entrez2 <- chip2_annot$geneId

annotations_edb2 <- AnnotationDbi::select(EnsDb.Hsapiens.v75,

keys = entrez2,

columns = c(“GENENAME”),

keytype = “ENTREZID”)

FIGURE 6.15  Distribution of Poly II relative to the TSS.