Man pages for detectRUNS
Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes
| chromosomeLength | Function to found max position for each chromosome |
| consecutiveRuns | Function to detect consecutive runs in a vector (individual's... |
| consecutiveRunsCpp | Function to detect consecutive runs in a vector (individual's... |
| consecutiveRUNS.run | Main function to detect genomic RUNS (ROHom/ROHet) using the... |
| createRUNdf | Function to create a dataframe of RUNS per individual animal... |
| 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 |
| genoConvert | Convert 0/1/2 genotypes to 0/1 |
| genoConvertCpp | Convert 0/1/2 genotypes to 0/1 |
| heteroZygotTest | Function to check whether a window is (loosely) heterozygous... |
| heteroZygotTestCpp | Function to check whether a window is (loosely) heterozygous... |
| homoZygotTest | Function to check whether a window is (loosely) homozygous or... |
| homoZygotTestCpp | Function to check whether a window is (loosely) homozygous or... |
| 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_PatternRuns | Plot sum of run-lengths (or average run-lengths) against the... |
| 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 | Function to detect runs using sliding window approach |
| slidingRUNS.run | Main function to detect RUNS (ROHom/ROHet) using sliding... |
| slidingWindow | Function to slide a window over a vector (individual's... |
| slidingWindowCpp | Function to slide a window over a vector (individual's... |
| snpInRun | Function to return a vector of T/F for whether a SNP is or... |
| snpInRunCpp | Function to return a vector of T/F for whether a SNP is or... |
| 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 |
