poppr (version 2.1.1)

win.ia: Calculate windows of the index of association for genlight objects.

Description

Genlight objects can contain millions of loci. Since it does not make much sense to calculate the index of association over that many loci, this function will scan windows across the loci positions and calculate the index of association.

Usage

win.ia(x, window = 100L, min.snps = 3L, threads = 1L, quiet = FALSE)

Arguments

x

a genlight or snpclone object.

window

an integer specifying the size of the window.

min.snps

an integer specifying the minimum number of snps allowed per window. If a window does not meet this criteria, the value will return as NA.

threads

The maximum number of parallel threads to be used within this function. A value of 0 (default) will attempt to use as many threads as there are available cores/CPUs. In most cases this is ideal. A value of 1 will force the function to run serially, which

quiet

if FALSE, a progress bar will be printed to the screen.

Value

• Index of association representing the samples in this genlight object.

See Also

genlight, snpclone, samp.ia, ia, bitwise.dist

Examples

# with structured snps assuming 1e4 positions
set.seed(999)
x <- glSim(n.ind = 10, n.snp.nonstruc = 5e2, n.snp.struc = 5e2, ploidy = 2)
position(x) <- sort(sample(1e4, 1e3))
res <- win.ia(x, window = 300L) # Calculate for windows of size 300
plot(res, type = "l")

# unstructured snps
set.seed(999)
x <- glSim(n.ind = 10, n.snp.nonstruc = 1e3, ploidy = 2)
position(x) <- sort(sample(1e4, 1e3))
res <- win.ia(x, window = 300L) # Calculate for windows of size 300
plot(res, type = "l")