tab2geo: Create a 'ggene' object from data frames

In ggene: Semivariogram and Exploratory Spatial Analysis of Genetic Data

Description

The function create a ggene object from a data frame containing the genetic data and a second data frame containing the coordinates.

Usage

tab2geo(X, coord)

Arguments

X	A data frame with the genetic data of a set of individuals. Locus in columns, individuals as rows.
coord	A data frame containing the coordinates of the individuals.

Details

tab2geo was written to handle haploid data which are not supported in the function gene2geo.

Value

An object of class ggene with 5 items:

tab	Data frame of the dummy variable coding for the presence of each allele. The number of rows is the number of individuals, the number of columns is the total number of alleles (all locus pooled).
coord	The x and y cordinates (longitude and latitude).
nloc	Number of different locus.
loc	The number of different alleles per locus.
locnames	The names of the different locus.

Warning

Caution is needed as regards missing data (NAs). NAs must be removed or replaced prior to analysing the dataset. One option developped in the package adegenet is to replace NAs by the NAs by the mean allele frequency. ggene has no function to handle NAs in raw data and users are referred to the package adegenet and its function scaleGen. This function will allow processing diploid data as a genind object. For haploid datasets, NAs removal must be done directly by users.

Author(s)

Jean-Pierre Rossi <[e-mail]>

See Also

tab2geo

Examples

dat <- read.csv(system.file("extdata/sim_01.csv", package="ggene"),
 header=FALSE)
xy <- read.csv(system.file("extdata/xysim_01.csv", package="ggene"),
 header=FALSE)
data <- tab2geo(X=dat, coord=xy)
class(data)
str(data)

ggene documentation built on May 2, 2019, 5:54 p.m.