Usage
read.Structure(infile, missingin = -9, missingout = -9, sep = "",
markernames = TRUE, labels = TRUE, extrarows = 1, extracols = 0,
ploidy = 4, getexcols = FALSE)
- infile
{
Character string. The file path to be read.
}
- missingin
{
The symbol used to represent missing data in the Structure file.
}
- missingout
{
The symbol to be used to represent missing data in the genotype object
that is produced.
}
- sep
{
The character used to delimit the fields of the Structure file (tab by default).
}
- markernames
{
Boolean, indicating whether the file has a header containing marker names.
}
- labels
{
Boolean, indicating whether the file has a column containing sample names.
}
- extrarows
{
Integer. The number of extra rows that the file has, not counting
marker names. This could include rows for recessive alleles,
inter-marker distances, or phase information.
}
- extracols
{
Integer. The number of extra columns that the file has, not counting
sample names (labels). This could include PopData, PopFlag, LocData,
Phenotype, or any other extra columns.
}
- ploidy
{
Integer. The ploidy of the file, i.e. how many rows there are for each
individual.
}
- getexcols
{
Boolean, indicating whether the function should return the data from any
extra columns.
}
The current version of read.Structure does not support the
ONEROWPERIND option in the file format. Each locus must only have one
column. If your data is in ONEROWPERIND format, it should be fairly
simple to manipulate it in a spreadsheet program so that it can be read
by read.GeneMapper instead.
read.Structure uses read.table to initially read the file into a
data frame, then extracts information from the data frame. Because of
this, any header rows (particularly the one containing marker names)
should have leading tabs (or spaces if sep="") so that the marker
names align correctly with their corresponding genotypes. You should be
able to open the file in a spreadsheet program and have everything align
correctly.
If the file does not contain sample names, set labels=FALSE. The
samples will be numbered instead, and if you like you can edit the
dimnames of the genotype object after the fact if you have the
sample names stored separately. Likewise, if markernames=FALSE, the
loci will be numbered automatically by the column names that
read.table creates, but these can also be edited after the fact.
If getexcols=FALSE, the function returns only a genotype object in the
standard polysat format. This is a two-dimensional list, where samples
are represented in the first dimension and loci in the second
dimension. Each element of the list is an integer vector containing all
unique alleles for a given locus and sample.
If getexcols=TRUE, the function returns a list with two elements. The
first, named ExtraCol, is a data frame, where the row names are the
sample names and each column is one of the extra columns from the file
(but with each sample only once instead of being repeated ploidy
number of times). The second element is named Genotypes and is the
genotype object described above.
http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.3/structure_doc.pdf
Hubisz, M. J., Falush, D., Stephens, M. and Pritchard, J. K. (2009)
Inferring weak population structure with the assistance of sample
group information. Molecular Ecology Resources 9,
1322-1332.
Falush, D., Stephens, M. and Pritchard, J. K. (2007)
Inferences of population structure using multilocus genotype data:
dominant markers and null alleles. Molecular Ecology Notes
7, 574-578.
[object Object]
write.Structure, read.GeneMapper,
read.Tetrasat, read.ATetra,
read.GenoDive, dominant.to.codominant,
read.SPAGeDi
# create a file to read (normally done in a text editor or spreadsheet
# software)
cat("",
"-9-9-9-9-9-9-9-9",
"WIN1B",
"WIN1B",
"WIN1B",
"WIN1B",
"WIN1B-9-9-9-9-9-9-9-9",
"WIN1B-9-9-9-9-9-9-9-9",
"WIN1B-9-9-9-9-9-9-9-9",
"WIN1B-9-9-9-9-9-9-9-9",
"MCD1",
"MCD1",
"MCD1",
"MCD1",
"MCD1",
"MCD1",
"MCD1-9-9-9-9-9-9-9-9",
"MCD1-9-9-9-9-9-9-9-9",
"MCD2",
"MCD2",
"MCD2",
"MCD2",
"MCD2",
"MCD2",
"MCD2",
"MCD2",
"MCD3",
"MCD3