genind constructor {adegenet} | R Documentation |
Constructor for genind objects.
The function genind
creates a genind object from
a matrix of allelic frequency where genotypes are in rows and alleles
in columns. This table must have correct names for rows and
columns.
The function as.genind
is an alias for genind
function.
is.genind
tests if an object is a valid genind object.
Note: to get the manpage about genind, please type 'class ? genind'.
genind(tab,pop=NULL,prevcall=NULL, ploidy=2, type=c("codom","PA")) as.genind(tab,pop=NULL,prevcall=NULL, ploidy=2, type=c("codom","PA")) is.genind(x)
tab |
A table corresponding to the @tab slot of a genind object,
with individuals in rows and alleles in columns.
Its content depends on type (type of marker).- 'codom': table contains allele frequencies (numeric values summing to 1). - 'PA': table contains binary values, which indicate presence(1)/absence(0) of alleles. |
pop |
a factor giving the population of each genotype in 'x' |
prevcall |
call of an object |
ploidy |
an integer indicating the degree of ploidy of the genotypes. Beware: 2 is not an integer, but as.integer(2) is. |
type |
a character string indicating the type of marker: 'codom' stands for 'codominant' (e.g. microstallites, allozymes); 'PA' stands for 'presence/absence' (e.g. AFLP). |
x |
an object |
For genind
and as.genind
, a genind object. For is.genind
, a logical.
Thibaut Jombart t.jombart@imperial.ac.uk
"genind"
, and import2genind
for
importing from various types of file.
data(nancycats) nancycats@loc.names # isolate one marker, fca23 obj <- seploc(nancycats)$"fca23" obj