Subset data by population — popsub • poppr

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
)

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.

Value

A genind object or a matrix.

Author

Zhian N. Kamvar

Examples

# Load the dataset microbov.
data(microbov)

# List the population names.
popNames(microbov)
#>  [1] "Borgou"          "Zebu"            "Lagunaire"       "NDama"          
#>  [5] "Somba"           "Aubrac"          "Bazadais"        "BlondeAquitaine"
#>  [9] "BretPieNoire"    "Charolais"       "Gascon"          "Limousin"       
#> [13] "MaineAnjou"      "Montbeliard"     "Salers"         

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

# \dontrun{
# 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"))
# }