read.structure | R Documentation |
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.
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, sep = NULL, ask = TRUE, quiet = FALSE )
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. |
sep |
a character string used as separator between alleles. |
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). |
quiet |
logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE). |
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
.
an object of the class genind
Thibaut Jombart t.jombart@imperial.ac.uk
Pritchard, J.; Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155: 945-959
import2genind
, df2genind
,
read.fstat
, read.genetix
,
read.genepop
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
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.