detectRUNS0.9.6 package

Summary statistics on detected runs

Function to retrieve most common runs in the population

Function to write out RUNS per individual animal

Function to count number of times a SNP is in a RUN

Function to count number of times a SNP is in a RUN

Function to found max position for each chromosome

Function to detect consecutive runs in a vector (individual's genotype...

Main function to detect genomic RUNS (ROHom/ROHet) using the consecuti...

Function to detect consecutive runs in a vector (individual's genotype...

Function to create a dataframe of RUNS per individual animal Requires ...

Function to calculate oppositeAndMissingGenotypes array

Function to calculated Froh genome-wide or chromosome-wide

Function to calculated Froh using a ROH-class

Convert 0/1/2 genotypes to 0/1

Convert 0/1/2 genotypes to 0/1

Function to check whether a window is (loosely) heterozygous or not

Function to check whether a window is (loosely) heterozygous or not

Function to check whether a window is (loosely) homozygous or not

Function to check whether a window is (loosely) homozygous or not

Convert ped genotypes to 0/1

Plot Distribution of runs

Plot Froh-based inbreeding coefficients by group

Plot the proportion of times SNPs are inside runs - MANHATTAN PLOT

Plot sum of run-lengths (or average run-lengths) against the number of...

Function to plot runs per individual

Plot the number of times each SNP falls inside runs

Plot stacked runs

Violin plot of run length per individual (either sum or mean)

Read runs from external files

Function to return a dataframe of population (POP, ID)

Function to reorder data frames by CHROMOSOME

Function to detect runs using sliding window approach

Main function to detect RUNS (ROHom/ROHet) using sliding windows (a la...

Function to slide a window over a vector (individual's genotypes)

Function to slide a window over a vector (individual's genotypes)

Function to return a vector of T/F for whether a SNP is or not in a RU...

Function to return a vector of T/F for whether a SNP is or not in a RU...