gen_errors takes a raw data file and generates genotyping error outputs
which are written to csv file.
gen_errors(filename, replicates = TRUE, suffix = "_dup")File name of raw data input csv as a character string.
Logical. TRUE if replicates are present in the raw data.
File suffix to denote sample replicates. Default is the character string"_dup", change if required. Ignore if replicates = FALSE.
It will write to csv file genotype error file csv's for further processing and/or evaluation.
When run it calculates genotyping errors on the complete raw data set which it reads in from the `source/` sub-directory. The raw data expected is SNP genotypes generated through the Agena Bioscience MassARRAY genotyping system as provided by the Australian Genome Research Facility (AGRF).
Outputs are written to csv file to the `results/` sub-directory as:
numerical_alleles.csv
sample_error_results.csv
summary_error_results.csv
The genotyping error rates (sample amplification rate and, when replicate samples provided, allelic dropout and false allele rates) are used in downstream processes and are further refined.
if (FALSE) {
gen_errors(filename = "CAGRF20021407_raw.csv", suffix = "_dup")
}