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Read Sample Data

Source: R/sample_data.R
read_sample_data.Rd

Reads sample data, including Arriba fusions, Arriba plots, Salmon counts, DRAGEN fusions, DRAGEN mapping metrics, Manta SVs, PURPLE CNVs, and PCGR SNVs.

Usage

read_sample_data(p, results_dir, tx2gene = NULL)

Arguments

p

RNAsum params list.

results_dir

Directory to output extracted Arriba PNGs to (created automatically if it does not already exist).

tx2gene

data.frame with tx_name and gene_id columns. Required for salmon. See tximport::tximport.

Value

A list of the input sample data.

Examples

p <- list(
  dragen_wts_dir = system.file("rawdata/test_data/dragen", package = "RNAsum"),
  arriba_dir = system.file("rawdata/test_data/dragen/arriba", package = "RNAsum"),
  umccrise = system.file(
    "rawdata/test_data/umccrised/test_sample_WGS",
    package = "RNAsum"
  )
)
res <- read_sample_data(p, tempdir())