read.loci {pegas}R Documentation

Read Allelic Data Files

Description

This function reads allelic data from a text file: rows are individuals, and each column is an allele. By default, the header of the file gives the locus names. If one column is labelled ``population'', it is taken as a population variable.

Usage

read.loci(file, header = TRUE, loci.sep = " ", allele.sep = "/",
          col.pop = "none", col.loci = NULL, skip = 0)

Arguments

file a file name specified by either a variable of mode character, or a quoted string.
header a logical specifying whether the first line of the data file gives the names of the loci (TRUE by default).
loci.sep the character(s) separating the loci (columns) in the data file (a space by default).
allele.sep the character(s) separating the alleles for each locus in the data file (a slash by default).
col.pop specifies whether one of the column of the data file identifies the population; default "none", otherwise an integer giving the number of the column.
col.loci a vector of integers specifying the indices of the columns that are loci. By default, all columns are taken as loci except one labelled "population", if present.
skip an integer specifying the number of lines in the data file to be skipped before reading the data.

Details

The rownames of the returned object identify the individual genotypes; they are either taken from the data file if present, or given the values "1", "2", ...

In the returned object, alleles are separated by "/", even if it is not the case in the data file.

Value

a data frame with class c("loci", "data.frame"). Details on the structure can be found in http://ape.mpl.ird.fr/pegas/DefinitionDataClassesPegas.pdf

Author(s)

Emmanuel Paradis

See Also

read.gtx, write.loci


[Package pegas version 0.1 Index]