poppr (version 2.9.6)

popsub: Subset data by population

Description

Create a new dataset with specified populations or exclude specified populations from the dataset.

Usage

popsub(
  gid,
  sublist = "ALL",
  exclude = NULL,
  blacklist = NULL,
  mat = NULL,
  drop = TRUE
)

Value

A genind object or a matrix.

Arguments

gid

a genind, genclone, genlight, or snpclone object.

sublist

a vector of population names or indexes that the user wishes to keep. Default to "ALL".

exclude

a vector of population names or indexes that the user wishes to discard. Default to NULL.

blacklist

DEPRECATED, use exclude.

mat

a matrix object produced by mlg.table to be subsetted. If this is present, the subsetted matrix will be returned instead of the genind object

drop

logical. If TRUE, unvarying alleles will be dropped from the population.

Author

Zhian N. Kamvar

Examples

# Load the dataset microbov.
data(microbov)

# List the population names.
popNames(microbov)

# Analyze only the populations with exactly 50 individuals
mic.50 <- popsub(microbov, sublist=c(1:6, 11:15), exclude=c(3,4,13,14))

if (FALSE) {
# Analyze the first 10 populations, except for "Bazadais"
mic.10 <- popsub(microbov, sublist=1:10, exclude="Bazadais")

# Take out the two smallest populations
micbig <- popsub(microbov, exclude=c("NDama", "Montbeliard"))

# Analyze the two largest populations
miclrg <- popsub(microbov, sublist=c("BlondeAquitaine", "Charolais"))
}