Creates a set of realistic mock files that can be used to test the molpathR import pipeline. Files include VCF, XML, text-based PDF-like reports, a survival CSV, and a tiny FASTQ file.
Usage
mp_example_files(dir = tempdir(), seed = 42)Arguments
- dir
Character. Directory where files are written. Default
tempdir().- seed
Integer. Random seed for reproducibility. Default
42.
Value
A named list of file paths:
- vcf
Character vector of 5 VCF file paths.
- xml
Character vector of 5 XML report file paths.
Character vector of 5 text-based mock PDF report paths.
- survival
Path to the survival CSV file.
- fastq
Path to the sample FASTQ file.
Examples
# \donttest{
files <- mp_example_files()
readLines(files$vcf[1], n = 5)
#> [1] "##fileformat=VCFv4.2"
#> [2] "##source=molpathR_synthetic_v0.1"
#> [3] "##reference=GRCh38"
#> [4] "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">"
#> [5] "##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">"
# }