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Fetch raw RNA-seq data from SRA

Source: R/01_ingest.R
mx_fetch_sra.Rd

Downloads pre-quantified count matrices for SRA project IDs using the recount3 package. This avoids computationally expensive local alignment while ensuring uniform processing across studies (Collado-Torres et al. 2017; Wilks et al. 2021).

Usage

mx_fetch_sra(srp_ids, cache_dir = tempdir(), organism = "human")

Arguments

srp_ids

Character vector of SRA project IDs (e.g., "SRP123456").

cache_dir

Character scalar. Directory for caching downloaded files.

organism

Character scalar. Species for the studies. Default: "human". (Note: recount3 uses "human" or "mouse").

Value

A named list of metaXpressStudy objects.

References

Wilks, C. et al. (2021) recount3: summaries and queries for large-scale RNA-seq expression and splicing. Genome Biology, 22(1), 323. doi:10.1186/s13059-021-02533-6

See also

mx_fetch_geo, mx_load_local

Examples

if (FALSE) { # \dontrun{
  studies <- mx_fetch_sra("SRP123456")
} # }