graph_to_pcs: Simulate PCs under an admixture graph

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Simulate PCs under an admixture graph

Description

This function simulates PCA of allele frequencies under an admixture graph model

Usage

graph_to_pcs(
  graph,
  nsnps = 10000,
  drift_default = 0.02,
  admix_default = 0.5,
  leaves_only = TRUE
)

Arguments

graph	An admixture graph as igraph object, or as edge list data frame with a column weight, as returned by qpgraph()$edges
nsnps	Number of SNPs to simulate
drift_default	Default branch lengths. Ignored if graph is a data frame with weights
admix_default	Default admixture weights. Ignored if graph is a data frame with weights
leaves_only	Return PCs for leaf nodes only

Value

A data frame with PCs for each population

See Also

graph_to_afs

Examples

## Not run: 
pcs = graph_to_pcs(example_igraph)
pcs %>% ggplot(aes(PC1, PC2, label = pop)) + geom_text() + geom_point()

## End(Not run)

uqrmaie1/admixtools documentation built on Nov. 3, 2024, 12:56 a.m.