Man pages for detectRUNS
Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes

chromosomeLengthFunction to found max position for each chromosome
consecutiveRunsFunction to detect consecutive runs in a vector (individual's...
consecutiveRunsCppFunction to detect consecutive runs in a vector (individual's...
consecutiveRUNS.runMain function to detect genomic RUNS (ROHom/ROHet) using the...
createRUNdfFunction to create a dataframe of RUNS per individual animal...
findOppositeAndMissingFunction to calculate oppositeAndMissingGenotypes array
Froh_inbreedingFunction to calculated Froh genome-wide or chromosome-wide
Froh_inbreedingClassFunction to calculated Froh using a ROH-class
genoConvertConvert 0/1/2 genotypes to 0/1
genoConvertCppConvert 0/1/2 genotypes to 0/1
heteroZygotTestFunction to check whether a window is (loosely) heterozygous...
heteroZygotTestCppFunction to check whether a window is (loosely) heterozygous...
homoZygotTestFunction to check whether a window is (loosely) homozygous or...
homoZygotTestCppFunction to check whether a window is (loosely) homozygous or...
pedConvertCppConvert ped genotypes to 0/1
plot_DistributionRunsPlot Distribution of runs
plot_InbreedingChrPlot Froh-based inbreeding coefficients by group
plot_manhattanRunsPlot the proportion of times SNPs are inside runs - MANHATTAN...
plot_PatternRunsPlot sum of run-lengths (or average run-lengths) against the...
plot_RunsFunction to plot runs per individual
plot_SnpsInRunsPlot the number of times each SNP falls inside runs
plot_StackedRunsPlot stacked runs
plot_ViolinRunsViolin plot of run length per individual (either sum or mean)
readExternalRunsRead runs from external files
readPOPCppFunction to return a dataframe of population (POP, ID)
reorderDFFunction to reorder data frames by CHROMOSOME
slidingRunsFunction to detect runs using sliding window approach
slidingRUNS.runMain function to detect RUNS (ROHom/ROHet) using sliding...
slidingWindowFunction to slide a window over a vector (individual's...
slidingWindowCppFunction to slide a window over a vector (individual's...
snpInRunFunction to return a vector of T/F for whether a SNP is or...
snpInRunCppFunction to return a vector of T/F for whether a SNP is or...
snpInsideRunsFunction to count number of times a SNP is in a RUN
snpInsideRunsCppFunction to count number of times a SNP is in a RUN
summaryRunsSummary statistics on detected runs
tableRunsFunction to retrieve most common runs in the population
writeRUNFunction to write out RUNS per individual animal
detectRUNS documentation built on Feb. 6, 2018, 5:01 p.m.