countIBS {CrypticIBDcheck} | R Documentation |
Returns counts of the number of markers at which a pair of subjects shares 0, 1 or 2 alleles identical-by-state (IBS), for all possible pairs. Counts for a given pair exclude markers where either pair member is missing data.
countIBS(x)
x |
An object of type |
IBS0 |
An upper triangular matrix whose (i,j)th element (i<j) is the count of non-missing markers where the ith and jth subjects share 0 alleles IBS. |
IBS1 |
An upper triangular matrix whose (i,j)th element (i<j) is the count of non-missing markers where the ith and jth subjects share 1 allele IBS. |
IBS2 |
An upper triangular matrix whose (i,j)th element (i<j) is the count of non-missing markers where the ith and jth subjects share 2 alleles IBS. |
Annick Joelle Nembot-Simo, Jinko Graham and Brad McNeney
data(Nhlsim) countIBS(Nhlsim$snp.data[1:5,])