slidingWindowCpp function

Function to slide a window over a vector (individual's genotypes)

This is a core function. The functions to detect RUNS are slid over the genome

slidingWindowCpp(data, gaps, windowSize, step, maxGap, ROHet = TRUE,
  maxOppositeGenotype = 1L, maxMiss = 1L)

Arguments

• data: vector of 0/1/2 genotypes
• gaps: vector of differences between consecutive positions (gaps) in bps
• windowSize: size of window (n. of SNP)
• step: by which (how many SNP) is the window slid
• maxGap: max distance between consecutive SNP in a window to be still considered a potential run
• ROHet: shall we detect ROHet or ROHom?
• maxOppositeGenotype: max n. of homozygous/heterozygous SNP
• maxMiss: max. n. of missing SNP

Returns

vector of TRUE/FALSE (whether a window is homozygous or NOT)