data-raw/chr11_genes.R

In argschwind/TAPseq: Targeted scRNA-seq primer design for TAP-seq

library(rtracklayer)

## download GENCODE hg38 annotations, filter for exons of protein-coding genes in chr11 region

# import gencode hg38 annotations
annot_url <- "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.annotation.gtf.gz"
annot <- import(annot_url, format = "gtf")

# only retain exons of protein-coding genes
exons <- annot[annot$type == "exon" &
                 annot$gene_type == "protein_coding" &
                 annot$transcript_type == "protein_coding"
               ]

# expressed genes from chr11 region
expr_genes <- c("AKIP1", "ARFIP2", "BET1L", "C11orf58", "CARS", "CD151", "CD81", "CHID1", "COPB1",
  "CSNK2A3", "CTR9", "CTSD", "DEAF1", "EIF3F", "EIF4G2", "FAR1", "GTF2H1", "HRAS", "HTATIP2",
  "IFITM1", "IFITM2", "ILK", "IPO7", "LDHA", "MOB2", "MRPL17", "MRPL23", "NAP1L4", "NCR3LG1",
  "NUCB2", "NUP98", "PDE3B", "PGAP2", "PHRF1", "PKP3", "PNPLA2", "POLR2L", "PRMT3", "PSMA1",
  "PSMD13", "RASSF7", "RHOG", "RIC8A", "RNH1", "RPL27A", "RPLP2", "RPS13", "RRAS2", "RRM1", "RRP8",
  "SAAL1", "SIGIRR", "SIRT3", "SLC25A22", "SPTY2D1", "STIM1", "SVIP", "TALDO1", "TEAD1", "TIMM10B",
  "TMEM41B", "TMEM9B", "TOLLIP", "TPP1", "TRIM5", "TSG101", "TSPAN4", "TSSC4", "USP47",
  "WEE1", "ZBED5", "ZNF143", "ZNF195", "ZNF215", "HBB", "HBD", "HBE1", "HBG1", "HBG2")

# only select exons of expressed genes
chr11_genes <- exons[exons$gene_name %in% expr_genes]

# save data as RData files in data directory
usethis::use_data(chr11_genes, overwrite = TRUE)