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Download raw FASTQ files for a SCOUT SPN from ENA

get_fastq.Rd

Downloads one or more FASTQ files from the ENA accession PRJEB97253 using the EBI FTP server. Files are cached locally and re-used on subsequent calls.

Usage

get_fastq(
  spn,
  sample = NULL,
  purity = NULL,
  read = "both",
  cache_dir = .ena_cache_dir(spn)
)

Arguments

spn

SPN identifier, e.g. "SPN01".

sample

Sample identifier, e.g. "1.1". Use NULL for normal files.

purity

Tumour purity: "0.9", "0.6", or "0.3". Required when sample is not NULL.

read

Read direction: "R1", "R2", or "both" (default).

cache_dir

Local directory to store downloaded files. Defaults to ~/.cache/SCOUT/<spn>/fastq/.

Value

Invisible named character vector of local file paths (names are "R1" and/or "R2").

Examples

if (FALSE) { # \dontrun{
# Download R1 and R2 for SPN01 sample 1.1 purity 0.9
paths <- get_fastq("SPN01", sample = "1.1", purity = "0.9")
paths$R1
paths$R2

# Download normal files
get_fastq("SPN01", sample = NULL)
} # }