Find closest gene

closest_gene.R

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
g <- genes(txdb)
library(org.Hs.eg.db)
g$symbol <- mapIds(org.Hs.eg.db, g$gene_id, "SYMBOL", "ENTREZID")

library(plyranges)
query <- data.frame(
  seqnames=c("chr1","chr2","chr3"),
  start=50e6, end=50e6) %>%
  as_granges()

query %>% join_nearest(g)

# if you want TSS:

tss <- g %>% anchor_5p() %>% mutate(width=1)
query %>% join_nearest(tss)

# if you want the gene position also in the output:

g_start_end <- g %>% mutate(gene_start = start, gene_end = end)
query %>% join_nearest(g_start_end, distance=TRUE)