Calculate strain distribution pattern from SNP genotypes
Calculate the strain distribution patterns (SDPs) from the strain genotypes at a set of SNPs.
calc_sdp(geno)
geno |
Matrix of SNP genotypes, markers x strains, coded as 1 (AA) and 3 (BB). Markers with values other than 1 or 3 are omitted, and monomorphic markers, are omitted. |
A vector of strain distribution patterns: integers between 1 and 2^n - 2 where n is the number of strains, whose binary representation indicates the strain genotypes.
x <- rbind(m1=c(3, 1, 1, 1, 1, 1, 1, 1),
m2=c(1, 3, 3, 1, 1, 1, 1, 1),
m3=c(1, 1, 1, 1, 3, 3, 3, 3))
calc_sdp(x)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.