ad.correct {rCNV}

Correct allele depth values

Description

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(s)

Piyal Karunarathne

Examples

## Not run: adc<-ad.correct(ADtable)