library(tidyverse)
library(rtracklayer)
source("scripts/add_refseq.R")
argv <- commandArgs(trailingOnly = TRUE)
input <- argv[1]
release <- argv[2]
var <- paste0("Hs.Ensembl", release)
output <- paste0(var, ".RData")
anno <- import(input) %>%
as.data.frame %>%
filter(type == "transcript")
tx_2_all <- add_refseq(anno, "gene_id") %>%
dplyr::select(id = transcript_id,
ensembl_gene = gene_id,
symbol = gene_name,
entrez_id = entrezgene,
transcript_type = transcript_biotype)
# Save results
assign(var, tx_2_all)
save_cmd <- paste0("save(", var, ', file = "', output, '", compress = "xz")')
eval(parse(text = save_cmd))
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