apex (version 1.0.6)

multidna2genind: Convert multidna into genind

Description

The functions multidna2genind and multiphyDat2genind concatenates separate DNA alignments, and then extracts SNPs of the resulting alignment into a genind object.

Usage

multidna2genind(x, genes = TRUE, mlst = FALSE, gapIsNA = FALSE)
multiphyDat2genind(x, genes = TRUE, mlst = FALSE, gapIsNA = FALSE)

Value

a genind object

Arguments

x

a multidna or multiphyDat object.

genes

an optional vector indicating the genes to retain for the concatenation; any way to subset the list in x@dna or x@seq is acceptable; by default, all genes are used.

mlst

if TRUE, each gene will result in a single locus in the genind object. (Default to FALSE)

gapIsNA

if TRUE and mlst = TRUE, sequences that consist entirely of gaps will be considered as NAs. (Default to FALSE)

Author

Thibaut Jombart , Zhian N. Kamvar, Klaus Schliep

See Also

• concatenate

• DNAbin2genind to convert single DNAbin objects.

Examples

## simple conversion with nicely ordered output
data(woodmouse)
genes <- list(gene1=woodmouse[,1:500], gene2=woodmouse[,501:965])
x <- new("multidna", genes)
x
y <- multidna2multiphyDat(x)
y
z1 <- multidna2genind(x)
z1
z2 <- multiphyDat2genind(y)
all.equal(z1, z2)