A list containing example Axiom genotyping report data with header information and quality metrics from the Axiom genotyping platform.
Format
A list with 2 elements:
- header
Character vector with 9 elements containing metadata including chip type, library set information, processing parameters, and timestamps
- data
Data frame with 15 rows and 4 variables:
cel_files: Character. CEL file namestotal_call_rate: Numeric. Percentage of successful genotype callsaverage_heterozygosity: Numeric. Average heterozygosity ratemedian_intensity: Numeric. Median signal intensity
Examples
data(example_axiom_report)
example_axiom_report$header
#> [1] "#%chip_type=Axiom_GW_Hu_SNP"
#> [2] "#%lib_set_name=Axiom_GW_Hu_SNP.r2"
#> [3] "#%lib_set_version=r2"
#> [4] "#%affymetrix-algorithm-param-apt-time-str=May 23 14:30:45 2025"
#> [5] "#%create_date=2024-01-15T10:30:45Z"
#> [6] "#%guid=1234567890abcdef"
#> [7] "#%program_name=apt-probeset-genotype"
#> [8] "#%program_version=1.21.0"
#> [9] "#%program_company=Affymetrix"
head(example_axiom_report$data)
#> cel_files total_call_rate average_heterozygosity median_intensity
#> 1 Sample_001.CEL 97.5 0.230 2150
#> 2 Sample_002.CEL 94.2 0.285 1890
#> 3 Sample_003.CEL 98.1 0.215 2340
#> 4 Sample_004.CEL 96.8 0.250 2100
#> 5 Sample_005.CEL 93.5 0.305 1750
#> 6 Sample_006.CEL 99.2 0.220 2500
summary(example_axiom_report$data$total_call_rate)
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> 92.10 94.50 96.30 96.05 97.70 99.20