Simulate sequencing data and write them to a temporary FASTQ file — example_fastq • pepitope

Simulate sequencing data and write them to a temporary FASTQ file

Usage

example_fastq(
  samples,
  peptide_sheets,
  target_reads = 1000,
  custom = TRUE,
  seed = 91651
)

Arguments

samples: The .tsv or data.frame file containing sample information
peptide_sheets: A list, each item containing construct information
target_reads: How many reads to simulate on average
custom: Whether to add custom modifications to founds
seed: Seed for deterministic pseudo-random count generation

Value

The path to the created FASTQ file

Examples

samples = data.frame(sample_id="sample1", patient="pat1", rep="1",
    origin="library", barcode="GGG")
constructs = list(pat1=data.frame(gene_name="GENE1", mut_id="GENE1_A1V",
    pep_id="GENE1_A1V", pep_type="alt", tiled="ATGGCCGCC", barcode_1="AAAA"))
example_fastq(samples, constructs, target_reads=2, custom=FALSE)
#> [1] "/tmp/RtmpDX08iG/my_seqdata.fq"