Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes

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Documentation for package ‘detectRUNS’ version 0.9.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

consecutiveRUNS.run	Main function to detect genomic RUNS (ROHom/ROHet) using the consecutive method
consecutiveRunsCpp	Function to detect consecutive runs in a vector (individual's genotypes)
createRUNdf	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
findOppositeAndMissing	Function to calculate oppositeAndMissingGenotypes array
Froh_inbreeding	Function to calculated Froh genome-wide or chromosome-wide
Froh_inbreedingClass	Function to calculated Froh using a ROH-class
genoConvertCpp	Convert 0/1/2 genotypes to 0/1
heteroZygotTest	Function to check whether a window is (loosely) heterozygous or not
heteroZygotTestCpp	Function to check whether a window is (loosely) heterozygous or not
homoZygotTest	Function to check whether a window is (loosely) homozygous or not
homoZygotTestCpp	Function to check whether a window is (loosely) homozygous or not
pedConvertCpp	Convert ped genotypes to 0/1
plot_DistributionRuns	Plot Distribution of runs
plot_InbreedingChr	Plot Froh-based inbreeding coefficients by group
plot_manhattanRuns	Plot the proportion of times SNPs are inside runs - MANHATTAN PLOT
plot_PatternRuns	Plot sum of run-lengths (or average run-lengths) against the number of runs per individual
plot_Runs	Function to plot runs per individual
plot_SnpsInRuns	Plot the number of times each SNP falls inside runs
plot_StackedRuns	Plot stacked runs
plot_ViolinRuns	Violin plot of run length per individual (either sum or mean)
readExternalRuns	Read runs from external files
readPOPCpp	Function to return a dataframe of population (POP, ID)
reorderDF	Function to reorder data frames by CHROMOSOME
slidingRUNS.run	Main function to detect RUNS (ROHom/ROHet) using sliding windows (a la Plink)
slidingWindow	Function to slide a window over a vector (individual's genotypes)
slidingWindowCpp	Function to slide a window over a vector (individual's genotypes)
snpInRun	Function to return a vector of T/F for whether a SNP is or not in a RUN
snpInRunCpp	Function to return a vector of T/F for whether a SNP is or not in a RUN
snpInsideRuns	Function to count number of times a SNP is in a RUN
snpInsideRunsCpp	Function to count number of times a SNP is in a RUN
summaryRuns	Summary statistics on detected runs
tableRuns	Function to retrieve most common runs in the population
writeRUN	Function to write out RUNS per individual animal