slidingWindowCpp: Function to slide a window over a vector (individual's...

In detectRUNS: Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes

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)

detectRUNS documentation built on Oct. 30, 2019, 11:41 a.m.