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Download and cache a TCGA or TARGET expression dataset

LoadTCGA.Rd

Downloads a consolidated expression matrix and clinical metadata for a TCGA or TARGET project and caches the result locally as an .rds file. Subsequent calls with the same arguments load from the cache instantly without re-downloading.

Usage

LoadTCGA(
  project,
  data_type = c("rnaseq", "microarray"),
  backend = c("recount3", "TCGAbiolinks"),
  cache_dir = NULL,
  force_reload = FALSE
)

Arguments

project

Character scalar. Project ID, e.g. "TCGA-GBM", "TCGA-LGG", "TARGET-NBL". See SurvPlot for the full list of available projects.

data_type

"rnaseq" (default) or "microarray". "microarray" forces backend = "TCGAbiolinks" automatically.

backend

Download engine. "recount3" (default) fetches a single pre-consolidated matrix — fast and reliable. "TCGAbiolinks" downloads one file per patient from the GDC API — use only when recount3 does not carry the project or for microarray data.

cache_dir

Directory for the cached .rds file. Defaults to the OS user cache directory for scSidekick.

force_reload

Logical (default FALSE). When TRUE, deletes the existing .rds cache file and re-downloads the dataset from scratch. Useful after adding TCGAbiolinks or when the upstream data have been updated. The new download is cached as usual.

Value

A named list with:

expr_mat

Numeric matrix, genes × samples, log2(TPM + 1) values.

meta

Data frame of clinical metadata, one row per sample.

project

Project ID string.

data_type

Data modality used.

backend

Download engine used.

Details

The returned list can be passed directly to SurvMetaSummary to explore available clinical columns before calling SurvPlot.

See also

SurvMetaSummary, SurvPlot

Examples

if (FALSE) { # \dontrun{
gbm <- LoadTCGA("TCGA-GBM")
SurvMetaSummary(gbm$meta)
SurvPlot(expr_mat   = gbm$expr_mat,
         meta       = gbm$meta,
         genes      = c("YAP1", "S100A4"),
         time_col   = "OS",
         status_col = "status",
         facet_row  = "gender",
         facet_col  = "paper_IDH.status",
         output_file = "~/Desktop/GBM_survival/")
} # }