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)
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
Value
Returns the coverage corrected allele depth table similar to the
output of hetTgen
Author
Piyal Karunarathne
Examples
if (FALSE) adc<-ad.correct(ADtable)
