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prep_setup.R
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prep_setup.R
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## Download required files for prep_sample.R
suppressMessages(library('downloader'))
suppressMessages(library('devtools'))
## Check that output files are not present
stopifnot(!dir.exists('rse_temp'))
stopifnot(!any(file.exists('rse_gene.Rdata', 'rse_exon.Rdata', 'rse_jx.Rdata')))
stopifnot(!any(file.exists('counts_exon.tsv.gz', 'counts_gene.tsv.gz')))
## Helper function
down_file <- function(file_name, repo = 'recount-website') {
if(!file.exists(file_name)) {
url <- ifelse(repo == 'recount-website',
'https:/leekgroup/recount-website/raw/master/genes/',
ifelse(repo == 'recount-introns',
'https:/leekgroup/recount-website/raw/master/rse/',
'https:/nellore/runs/raw/master/gtex/')
)
download(paste0(url, file_name), dest = file_name, mode = 'wb')
} else {
message(paste(Sys.time(), 'using previously downloaded', file_name))
}
}
## Download files if necessary
bed <- 'Gencode-v25.bed'
count_groups_file <- 'count_groups.Rdata'
hg38 <- 'hg38.sizes'
introns <- 'introns_unique.Rdata'
down_file(bed)
down_file(count_groups_file)
down_file(hg38, repo = 'runs')
down_file(introns, repo = 'recount-introns')
## Reproducibility info
proc.time()
options(width = 120)
session_info()