strata-methods: Access and manipulate the population strata for genind or...

In adegenet: Exploratory Analysis of Genetic and Genomic Data

Access and manipulate the population strata for genind or genlight objects.

Description

The following methods allow the user to quickly change the strata of a genind or genlight object.

Usage

strata(x, formula = NULL, combine = TRUE, value)

strata(x) <- value

nameStrata(x, value)

nameStrata(x) <- value

splitStrata(x, value, sep = "_")

splitStrata(x, sep = "_") <- value

addStrata(x, value, name = "NEW")

addStrata(x, name = "NEW") <- value

Arguments

x	a genind or genlight object
formula	a nested formula indicating the order of the population strata.
combine	if TRUE (default), the levels will be combined according to the formula argument. If it is FALSE, the levels will not be combined.
value	a data frame OR vector OR formula (see details).
sep	a character indicating the character used to separate hierarchical levels. This defaults to "_".
name	an optional name argument for use with addStrata if supplying a vector. Defaults to "NEW".

Details

Function Specifics

• strata() - Use this function to view or define population stratification of a genind or genlight object.

• nameStrata() - View or rename the different levels of strata.

• splitStrata() - Split strata that are combined with a common separator. This function should only be used once during a workflow.

  • Rationale: It is often difficult to import files with several levels of strata as most data formats do not allow unlimited population levels. This is circumvented by collapsing all population strata into a single population factor with a common separator for each observation.

• addStrata() - Add levels to your population strata. This is ideal for adding groups defined by find.clusters. You can input a data frame or a vector, but if you put in a vector, you have the option to name it.

Argument Specifics

These functions allow the user to seamlessly carry all possible population stratification with their genind or genlight object. Note that there are two ways of performing all methods:

• modifying: strata(myData) <- myStrata

• preserving: myNewData <- strata(myData, value = myStrata)

They essentially do the same thing except that the modifying assignment method (the one with the "<-") will modify the object in place whereas the non-assignment method will preserve the original object (unless you overwrite it). Due to convention, everything right of the assignment is termed value. To avoid confusion, here is a guide to the argument value for each function:

• strata() value = a data.frame that defines the strata for each individual in the rows.

• nameStrata() value = a vector or a formula that will define the names.

• splitStrata() value = a formula argument with the same number of levels as the strata you wish to split.

• addStrata() value = a vector or data.frame with the same length as the number of individuals in your data.

Details on Formulas

The preferred use of these functions is with a formula object. Specifically, a hierarchical formula argument is used to assign the levels of the strata. An example of a hierarchical formula would be:

~Country/City/Neighborhood

This convention was chosen as it becomes easier to type and makes intuitive sense when defining a hierarchy. Note: it is important to use hiearchical formulas when specifying hierarchies as other types of formulas (eg. ~Country*City*Neighborhood) will give incorrect results.

Author(s)

Zhian N. Kamvar

See Also

setPop genind as.genind

Examples

# let's look at the microbov data set:
data(microbov)
microbov

# We see that we have three vectors of different names in the 'other' slot. 
# ?microbov
# These are Country, Breed, and Species
names(other(microbov))

# Let's set the strata
strata(microbov) <- data.frame(other(microbov))
microbov

# And change the names so we know what they are
nameStrata(microbov) <- ~Country/Breed/Species

## Not run: 
# let's see what the strata looks like by Species and Breed:
head(strata(microbov, ~Breed/Species))

# If we didn't want the last column combined with the first, we can set
# combine = FALSE
head(strata(microbov, ~Breed/Species, combine = FALSE))

#### USING splitStrata ####

# For the sake of example, we'll imagine that we have imported our data set
# with all of the stratifications combined. 
setPop(microbov) <- ~Country/Breed/Species
strata(microbov) <- NULL

# This is what our data would look like after import.
microbov

# To set our strata here, we need to use the functions strata and splitStrata
strata(microbov) <- data.frame(x = pop(microbov))
microbov # shows us that we have "one" level of stratification
head(strata(microbov)) # all strata are separated by "_"

splitStrata(microbov) <- ~Country/Breed/Species
microbov # Now we have all of our strata named and split
head(strata(microbov)) # all strata are appropriately named and split.

## End(Not run)

adegenet documentation built on Feb. 16, 2023, 6 p.m.