pairwisefst-class | R Documentation |
S4 class to represent a pairwise Fst results obtained with the compute.pairwiseFST
values
A data frame with npop*(npop-1)/2 rows and 3 (or 7 if blockjackknife is TRUE) columns containing for both the Fst and Q2, estimates over all the SNPs and if blockjackknife=TRUE, the estimated block-jackknife and standard error (s.e.). The seventh (or third if blockjackknife=FALSE) column gives the number of SNPs.
PairwiseFSTmatrix
A npxnp matrix containing the pairwise FST estimates
PairwiseSnpFST
A matrix (nsnp rows and npops columns) with read count data for the reference allele
PairwiseSnpQ1
A matrix (nsnp rows and npops columns) with overall read coverage
PairwiseSnpQ2
A matrix (nsnp rows and 4 columns) detailing for each SNP, the chromosome (or scaffold), the position, allele 1 and allele 2
blockjacknife
A logical indicating whether block-jackknife estimates of standard errors are available (TRUE) or not (FALSE)
To generate pairwise object, see compute.pairwiseFST
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