genotypeeval (version 1.2.2)

numberCalls: Total Calls. This is the total number of calls in the file (including MULTIs so hom ref, hom var and hom alt might not add up). These methods are private. Users are not expected to provide the number of hom ref and number of duplicate calls - these functions are generally called through the function VCFEvaluate

Description

Total Calls. This is the total number of calls in the file (including MULTIs so hom ref, hom var and hom alt might not add up). These methods are private. Users are not expected to provide the number of hom ref and number of duplicate calls - these functions are generally called through the function VCFEvaluate

Usage

numberCalls(x, n.hom, n.dup, ll, ul)

Arguments

x

myvcf of interest

n.hom

Number of homozygous reference. Pass so don't need to recalculate

n.dup

number of multi calls to add onto the total calls

ll

lower limit to pass for hom ref

ul

upper limit to pass for hom ref

Value

• list with name, logical (passed or not), numeric (total number of calls)