createRUNdf function

Function to create a dataframe of RUNS per individual animal Requires a map file (other filename to read or R object) Parameters on maximum number of missing and opposite genotypes in the run (not the window) are implemented here

createRUNdf(snpRun, mapFile, minSNP = 3, minLengthBps = 1000,
  minDensity = 1/10, oppositeAndMissingSNP, maxOppRun = NULL,
  maxMissRun = NULL)

Arguments

• snpRun: vector of TRUE/FALSE (is the SNP in a RUN?)
• mapFile: Plink-like map file (data.frame)
• minSNP: minimum n. of SNP to call a RUN
• minLengthBps: minimum length of run in bps (defaults to 1000 bps = 1 kbps)
• minDensity: minimum n. of SNP per kbps (defaults to 0.1 = 1 SNP every 10 kbps)
• oppositeAndMissingSNP: indexed array of missing and opposite genotypes (SNP order in the genome is the index)
• maxOppRun: max n. of opposite genotype SNPs in the run (not in the window!)
• maxMissRun: max n. of missing SNPs in the run (not in the window!)

Returns

a data.frame with RUNS per animal