Generate Compatible Mock Dataset for RNA-seq Analysis

A convenience function to quickly generate a complete set of compatible mock files commonly used in RNA-seq alignment and quantification workflows.

Usage

sn_generate_rnaseq_dataset(
  output_dir = NULL,
  include_paired_reads = TRUE,
  genome_size = "small",
  read_count = "medium",
  compress = FALSE,
  seed = 123
)

Arguments

output_dir

Character. Directory to save files. If NULL, temporary files are created.

include_paired_reads

Logical. Whether to generate paired-end reads (default: TRUE).

genome_size

Character. Size of the reference genome: "minimal", "small", "medium".

read_count

Character. Number of reads to generate: "minimal", "small", "medium", "large".

compress

Logical. Whether to compress output files (default: FALSE for realistic workflow).

seed

Integer. Random seed for reproducible generation.

Value

Named list with paths to generated files: reference, reads_r1, reads_r2, annotation.

See also

Other mock data generation: sn_cleanup_mockdata_examples(), sn_generate_mockdata(), sn_generate_mockdata_batch(), sn_get_example_value_with_mockdata()

Examples

if (FALSE) { # \dontrun{
# Generate temporary compatible dataset
dataset <- sn_generate_rnaseq_dataset()

# Generate dataset in specific directory
dataset <- sn_generate_rnaseq_dataset(
  output_dir = "mock_rnaseq_data/",
  genome_size = "small",
  read_count = "medium"
)

# Use the files for alignment testing
print(dataset)
# $reference
# $reads_r1
# $reads_r2
# $annotation
} # }