write.freq.SPAGeDi: Create a File of Allele Frequencies for SPAGeDi

In polysat: Tools for Polyploid Microsatellite Analysis

Create a File of Allele Frequencies for SPAGeDi

Description

A table of allele frequencies such as that produced by simpleFreq or deSilvaFreq is used to calculate average allele frequencies for the entire dataset. These are then written in a format that can be read by the software SPAGeDi.

Usage

write.freq.SPAGeDi(freqs, usatnts, file = "", digits = 2,
                   pops = row.names(freqs),
  loci = unique(as.matrix(as.data.frame(strsplit(names(freqs), split =
  ".", fixed = TRUE), stringsAsFactors = FALSE))[1, ]))

Arguments

freqs	A data frame of population sizes and allele frequencies, such as that produced by simpleFreq or deSilvaFreq. Populations are in rows, and alleles are in columns. A column is needed containing population sizes in number of genomes; this may either be a single column called “Genomes” or multiple columns named by the locus and “Genomes”, sepearated by a period. All other columns contain allele frequencies. The column names for these should be the locus and allele separated by a period.
usatnts	An integer vector containing the lengths of the microsatellite repeats for the loci in the table. In most cases, if object is the "gendata" object used to generate freqs, then you should set usatnts = Usatnts(object). This is needed to convert allele names in the same way that write.SPAGeDi converts allele names.
file	The name of the file to write.
digits	The number of digits to use to represent each allele. This should be the same as that used in write.SPAGeDi, so that allele names are consistent between the two files.
pops	An optional character vector indicating a subset of populations from the table to use in calculating mean allele frequencies.
loci	An optional character vector indicating a subset of loci to write to the file.

Details

For some calculations of inter-individual relatedness and kinship coefficients, SPAGeDi can read a file of allele frequencies to use in the calculation. write.freq.SPAGeDi puts allele frequencies from polysat into this format.

A weighted average of allele frequencies is calculated across all populations (or those specified by pops). The average is weighted by population size as specified in the “Genomes” column of freqs.

Allele names are converted to match those produced by write.SPAGeDi. Alleles are divided by the numbers in usatnts in order to convert fragment length in nucleotides to repeat numbers. If necessary, 10^(digits-1) is repeatedly subtracted from all alleles until they can be represented using the right number of digits.

The file produced is tab-delimited and contains two columns per locus. The first column contains the locus name followed by all allele names, and the second column contains the number of alleles followed by the allele frequencies.

Value

A file is written but no value is returned.

Note

SPAGeDi can already estimate allele frequencies in a way that is identical to that of simpleFreq. Therefore, if you have allele frequencies produced by simpleFreq, there is not much sense in exporting them to SPAGeDi. deSilvaFreq, however, is a more advanced and accurate allele frequency estimation than what is available in SPAGeDi v1.3. write.freq.SPAGeDi exists primarily to export allele frequencies from deSilvaFreq.

Author(s)

Lindsay V. Clark

References

https://ebe.ulb.ac.be/ebe/SPAGeDi.html

Hardy, O. J. and Vekemans, X. (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2, 618-620.

See Also

write.SPAGeDi, deSilvaFreq

Examples

## Not run: 
# set up a genambig object to use in this example
mygen <- new("genambig", samples=c(paste("G", 1:30, sep=""),
                                   paste("R", 1:50, sep="")),
             loci=c("afrY", "ggP"))
PopNames(mygen) <- c("G", "R")
PopInfo(mygen) <- c(rep(1, 30), rep(2, 50))
mygen <- reformatPloidies(mygen, output="one")
Ploidies(mygen) <- 4
Usatnts(mygen) <- c(2, 2)

# randomly create genotypes according to pre-set allele frequencies
for(s in Samples(mygen, populations=1)){
    Genotype(mygen, s, "afrY") <-
        unique(sample(c(140, 142, 146, 150, 152), 4, TRUE,
                      c(.30, .12, .26, .08, .24)))
    Genotype(mygen, s, "ggP") <-
        unique(sample(c(210, 214, 218, 220, 222), 4, TRUE,
                      c(.21, .13, .27, .07, .32)))
}
for(s in Samples(mygen, populations=2)){
    Genotype(mygen, s, "afrY") <-
        unique(sample(c(140, 142, 144, 150, 152), 4, TRUE,
                      c(.05, .26, .17, .33, .19)))
    Genotype(mygen, s, "ggP") <-
        unique(sample(c(212, 214, 220, 222, 224), 4, TRUE,
                      c(.14, .04, .36, .20, .26)))
}

# write a SPAGeDi file
write.SPAGeDi(mygen, file="SPAGdataFreqExample.txt")

# calculate allele frequenies
myfreq <- deSilvaFreq(mygen, self = 0.05)

# write allele frequencies file
write.freq.SPAGeDi(myfreq, usatnts=Usatnts(mygen),
file="SPAGfreqExample.txt")

## End(Not run)

polysat documentation built on Aug. 23, 2022, 5:07 p.m.