homoZygotTest function

Function to check whether a window is (loosely) homozygous or not

This is a core function. Parameters on how to consider a window homozygous are here (maxHet, maxMiss)

homoZygotTest(x, gaps, maxHet, maxMiss, maxGap, i, windowSize)

Arguments

• x: vector of 0/1 genotypes (from genoConvert())
• gaps: vector of differences between consecutive positions (gaps) in bps
• maxHet: max n. of heterozygous SNP in a homozygous window
• maxMiss: max n. of missing in a window
• maxGap: max distance between consecutive SNP in a window to be still considered a potential run
• i: index along the genome (genome-vector for each individual)
• windowSize: size of window (n. of SNP)

Returns

a list: i) TRUE/FALSE (whether a window is heterozygous or NOT); ii) indexes of "opposite and missing" genotype