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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", "topics": [ "createRUNdf" ] }, { "page": "findOppositeAndMissing", "title": "Function to calculate oppositeAndMissingGenotypes array", "topics": [ "findOppositeAndMissing" ] }, { "page": "Froh_inbreeding", "title": "Function to calculated Froh genome-wide or chromosome-wide", "topics": [ "Froh_inbreeding" ] }, { "page": "Froh_inbreedingClass", "title": "Function to calculated Froh using a ROH-class", "topics": [ "Froh_inbreedingClass" ] }, { "page": "genoConvertCpp", "title": "Convert 0/1/2 genotypes to 0/1", "topics": [ "genoConvertCpp" ] }, { "page": "heteroZygotTest", "title": "Function to check whether a window is (loosely) heterozygous or not", "topics": [ "heteroZygotTest" ] }, { "page": "heteroZygotTestCpp", "title": "Function to check whether a window is (loosely) heterozygous or not", "topics": [ "heteroZygotTestCpp" ] }, { "page": "homoZygotTest", "title": "Function to check whether a window is (loosely) homozygous or not", "topics": [ "homoZygotTest" ] }, { "page": "homoZygotTestCpp", "title": "Function to check whether a window is (loosely) homozygous or not", "topics": [ "homoZygotTestCpp" ] }, { "page": "pedConvertCpp", "title": "Convert ped genotypes to 0/1", "topics": [ "pedConvertCpp" ] }, { "page": "plot_DistributionRuns", "title": "Plot Distribution of runs", "topics": [ "plot_DistributionRuns" ] }, { "page": "plot_InbreedingChr", "title": "Plot Froh-based inbreeding coefficients by group", "topics": [ "plot_InbreedingChr" ] }, { "page": "plot_manhattanRuns", "title": "Plot the proportion of times SNPs are inside runs - MANHATTAN PLOT", "topics": [ "plot_manhattanRuns" ] }, { "page": "plot_PatternRuns", "title": "Plot sum of run-lengths (or average run-lengths) against the number of runs per individual", "topics": [ "plot_PatternRuns" ] }, { "page": "plot_Runs", 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