slidingWindowCpp {detectRUNS}

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

Description

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

Usage

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

Value

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