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Function to generate a random sample of reads in `.fastq` format

rreads.Rd

This function generates a specified number of random reads in `.fastq` format. Each read consists of a sequence identifier, a random DNA sequence, a separator line, and quality scores.

Usage

rreads(patient_id, n, read_length = 8)

Arguments

patient_id

A character string representing the patient ID.

n

An integer specifying the number of reads to generate.

read_length

An integer specifying the length of each read. It should be multiple of 4. Default is 8.

Value

A character vector containing the generated `.fastq` lines.

Details

The function generates random DNA sequences using the nucleotides A, T, G, and C. The quality scores are represented as ASCII characters, with 'I' indicating high quality. The output is formatted as a `.fastq` file, which consists of four lines per read:

  • Line 1: Sequence identifier (e.g., @patient_id_read1)

  • Line 2: Random DNA sequence

  • Line 3: Separator (e.g., +)

  • Line 4: Quality scores

@seealso create_empty_fastq for creating an empty `.fastq` file.

Examples

# Generate 5 random reads for patient ID "patient_123"
rreads("patient_123", n = 5)
#>  [1] "@patient_123_read1" "CCTGATGG"           "+"                 
#>  [4] "IIIIIIII"           "@patient_123_read2" "CATATGTC"          
#>  [7] "+"                  "IIIIIIII"           "@patient_123_read3"
#> [10] "ATACCTGA"           "+"                  "IIIIIIII"          
#> [13] "@patient_123_read4" "TTGTAAGT"           "+"                 
#> [16] "IIIIIIII"           "@patient_123_read5" "ACACCGCC"          
#> [19] "+"                  "IIIIIIII"          
# Generate 10 random reads for patient ID "patient_456" with a read length of 12
rreads("patient_456", n = 10, read_length = 12)
#>  [1] "@patient_456_read1"  "CGTGTGTGTCTA"        "+"                  
#>  [4] "IIIIIIIIIIII"        "@patient_456_read2"  "GTTGATCCACAG"       
#>  [7] "+"                   "IIIIIIIIIIII"        "@patient_456_read3" 
#> [10] "CTATTTGCTCTT"        "+"                   "IIIIIIIIIIII"       
#> [13] "@patient_456_read4"  "AGGCAAAATAAA"        "+"                  
#> [16] "IIIIIIIIIIII"        "@patient_456_read5"  "TCAGGACGGCTC"       
#> [19] "+"                   "IIIIIIIIIIII"        "@patient_456_read6" 
#> [22] "AGAGATAAAAGA"        "+"                   "IIIIIIIIIIII"       
#> [25] "@patient_456_read7"  "TGCGCTATTGCG"        "+"                  
#> [28] "IIIIIIIIIIII"        "@patient_456_read8"  "CATCACGACAGG"       
#> [31] "+"                   "IIIIIIIIIIII"        "@patient_456_read9" 
#> [34] "ATGCGGTCTACC"        "+"                   "IIIIIIIIIIII"       
#> [37] "@patient_456_read10" "GTCTATATGCAT"        "+"                  
#> [40] "IIIIIIIIIIII"