adegenet: df2genind – R documentation

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df2genind

Convert a data.frame of allele data to a genind object.

Description

The function df2genind converts a data.frame (or a matrix) into a genind object. The data.frame must meet the following requirements:

genotypes are in row (one row per genotype)
markers/loci are in columns
each element is a string of characters coding alleles, ideally separated by a character string (argument sep); if no separator is used, the number of characters coding alleles must be indicated (argument ncode).

Usage

df2genind(
  X,
  sep = NULL,
  ncode = NULL,
  ind.names = NULL,
  loc.names = NULL,
  pop = NULL,
  NA.char = "",
  ploidy = 2,
  type = c("codom", "PA"),
  strata = NULL,
  hierarchy = NULL,
  check.ploidy = getOption("adegenet.check.ploidy")
)

Arguments

`X`	a matrix or a data.frame containing allelle data only (see decription)
`sep`	a character string separating alleles. See details.
`ncode`	an optional integer giving the number of characters used for coding one genotype at one locus. If not provided, this is determined from data.
`ind.names`	optinal, a vector giving the individuals names; if NULL, taken from rownames of X. If factor or numeric, vector is converted to character.
`loc.names`	an optional character vector giving the markers names; if NULL, taken from colnames of X.
`pop`	an optional factor giving the population of each individual.
`NA.char`	a character string corresponding to missing allele (to be treated as NA)
`ploidy`	an integer indicating the degree of ploidy of the genotypes.
`type`	a character string indicating the type of marker: 'codom' stands for 'codominant' (e.g. microstallites, allozymes); 'PA' stands for 'presence/absence' markers (e.g. AFLP, RAPD).
`strata`	an optional data frame that defines population stratifications for your samples. This is especially useful if you have a hierarchical or factorial sampling design.
`hierarchy`	a hierarchical formula that explicitely defines hierarchical levels in your strata. see `hierarchy` for details.
`check.ploidy`	a boolean indicating if the ploidy should be checked (TRUE, default) or not (FALSE). Not checking the ploidy makes the import much faster, but might result in bugs/problems if the input file is misread or the ploidy is wrong. It is therefore advised to first import and check a subset of data to see if everything works as expected before setting this option to false.

Details

See genind2df to convert genind objects back to such a data.frame.

=== Details for the sep argument ===
this character is directly used in reguar expressions like gsub, and thus require some characters to be preceeded by double backslashes. For instance, "/" works but "|" must be coded as "\|".

Value

an object of the class genind for df2genind; a matrix of biallelic genotypes for genind2df

Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk, Zhian N. Kamvar kamvarz@science.oregonstate.edu

Examples

## simple example
df <- data.frame(locusA=c("11","11","12","32"),
locusB=c(NA,"34","55","15"),locusC=c("22","22","21","22"))
row.names(df) <- .genlab("genotype",4)
df

obj <- df2genind(df, ploidy=2, ncode=1)
obj
tab(obj)


## converting a genind as data.frame
genind2df(obj)
genind2df(obj, sep="/")

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