generate.jackknife.blocks: Generate block coordinates for block-jackknife

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

Generate block coordinates for block-jackknife

Description

Generate block coordinates for block-jackknife

Usage

generate.jackknife.blocks(x, nsnp.per.bjack.block, verbose = TRUE)

Arguments

x	A pooldata or countdata object containing SNP positions (snp.info slot)
nsnp.per.bjack.block	Number of consecutive SNPs of each block-jackknife block
verbose	If TRUE extra information is printed on the terminal

Value

A list with the two following elements:

1. "blocks.det": A matrix with three columns containing for each identified block (in row) the index of the start SNP, the index of the end SNP and the block Size in bp

2. "snp.block.id": A vector containing the blocks assigned to each SNP eligible for block-Jacknife (non eligible SNPs ares assigned NA)

3. "nblocks": A scalar corresponding to the number of blocks

4. "nsnps": Number of SNPs eligible for block-jackknife 'i.e., included in one block

Examples

make.example.files(writing.dir=tempdir())
pooldata=popsync2pooldata(sync.file=paste0(tempdir(),"/ex.sync.gz"),poolsizes=rep(50,15))
bjack.blocks=generate.jackknife.blocks(pooldata,nsnp.per.bjack.block=50)

poolfstat documentation built on Sept. 8, 2023, 5:49 p.m.