A function to correct depth values with odd number of coverage values due to sequencing anomalies or miss classification where genotype is homozygous and depth values indicate heterozygosity. The function adds a value of one to the allele with the lowest depth value for when odd number anomalies or make the depth value zero for when miss-classified. The genotype table must be provided for the latter.
Usage
ad.correct(
het.table,
gt.table = NULL,
odd.correct = TRUE,
verbose = TRUE,
parallel = FALSE
)Arguments
- het.table
allele depth table generated from the function
hetTgen- gt.table
genotype table generated from the function hetTgen
- odd.correct
logical, to correct for odd number anomalies in AD values. default
TRUE- verbose
logical. show progress. Default
TRUE- parallel
logical. whether to parallelize the process