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propTyped

Compute the proportion of typed elements

Description

The generic function propTyped is devoted to investigating the structure of missing data in adegenet objects.

Methods are defined for genind and genpop objects. They can return the proportion of available (i.e. non-missing) data per individual/population, locus, or the combination of both in with case the matrix indicates which entity (individual or population) was typed on which locus.

Usage

## S4 method for signature 'genind'
propTyped(x,  by=c("ind","loc","both"))
## S4 method for signature 'genpop'
propTyped(x,  by=c("pop","loc","both"))

Arguments

x

a genind and genpop object
by

a character being "ind","loc", or "both" for genind object and "pop","loc", or "both" for genpop object. It specifies whether proportion of typed data are provided by entity ("ind"/"pop"), by locus ("loc") or both ("both"). See details.

Details

When by is set to "both", the result is a matrix of binary data with entities in rows (individuals or populations) and markers in columns. The values of the matrix are 1 for typed data, and 0 for NA.

Value

A vector of proportion (when by equals "ind", "pop", or "loc"), or a matrix of binary data (when by equals "both")

Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

## Not run: 
data(nancycats)
propTyped(nancycats,by="loc")
propTyped(genind2genpop(nancycats),by="both")

## End(Not run)
adegenet

Exploratory Analysis of Genetic and Genomic Data

v2.1.3
GPL (>= 2)
Authors
Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)
Initial release

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