read.structure: Reading data from STRUCTURE

Description

The function read.structure reads STRUCTURE data files (.str ou .stru) and convert them into a genind object. By default, this function is interactive and asks a few questions about data content. This can be disabled (for optional questions) by turning the 'ask' argument to FALSE. However, one has to know the number of genotypes, of markers and if genotypes are coded on a single or on two rows before importing data.

Note: read.structure is meant for DIPLOID DATA ONLY. Haploid data with the STRUCTURE format can easily be read into R using read.table or read.csv and then converted using df2genind.

Usage

read.structure(file, n.ind=NULL, n.loc=NULL, onerowperind=NULL,
               col.lab=NULL, col.pop=NULL, col.others=NULL, row.marknames=NULL,
               NA.char="-9", pop=NULL, missing=NA, ask=TRUE, quiet=FALSE)

Arguments

file

a character string giving the path to the file to convert, with the appropriate extension.

n.ind

an integer giving the number of genotypes (or 'individuals') in the dataset

n.loc

an integer giving the number of markers in the dataset

onerowperind

a STRUCTURE coding option: are genotypes coded on a single row (TRUE), or on two rows (FALSE, default)

col.lab

an integer giving the index of the column containing labels of genotypes. '0' if absent.

col.pop

an integer giving the index of the column containing population to which genotypes belong. '0' if absent.

col.others

an vector of integers giving the indexes of the columns containing other informations to be read. Will be available in @other of the created object.

row.marknames

an integer giving the index of the row containing the names of the markers. '0' if absent.

NA.char

the character string coding missing data. "-9" by default. Note that in any case, series of zero (like "000") are interpreted as NA too.

pop

an optional factor giving the population of each individual.

ask

a logical specifying if the function should ask for optional informations about the dataset (TRUE, default), or try to be as quiet as possible (FALSE).

missing

can be NA, 0 or "mean". See details section.

quiet

logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE).

Value

an object of the class genind

encoding

UTF-8

Details

There are 3 treatments for missing values: - NA: kept as NA. - 0: allelic frequencies are set to 0 on all alleles of the concerned locus. Recommended for a PCA on compositionnal data. - "mean": missing values are replaced by the mean frequency of the corresponding allele, computed on the whole set of individuals. Recommended for a centred PCA.

References

Pritchard, J.; Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155: 945-959

Examples

Run this code

obj <- read.structure(system.file("files/nancycats.str",package="adegenet"),
  onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE)

obj

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