pairwisefst-class: S4 class to represent a pairwise Fst results obtained with...

In poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data

S4 class to represent a pairwise Fst results obtained with the compute.pairwiseFST

Description

S4 class to represent a pairwise Fst results obtained with the compute.pairwiseFST

Slots

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)

See Also

To generate pairwise object, see compute.pairwiseFST

poolfstat documentation built on April 4, 2025, 1:49 a.m.