clip.genepop: Remove designated markers from a GENEPOP file.

Description Usage Arguments Author(s) References Examples

Description

This function reads a GENEPOP file (Rousset 2008), remove designated markers, and write a GENEPOP file of clipped data. The user can directly designate the names of the markers to be removed. The user also can set the filtering threshold of major allele frequency.

Usage

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clip.genepop(infile, outfile, remove.list = NULL, major.af = NULL)

Arguments

infile

A character value specifying the name of the GENEPOP file to be clipped.

outfile

A character value specifying the name of the clipped GENEPOP file.

remove.list

A character value or vector specifying the names of the markers to be removed. The names must be included in the target GENEPOP file.

major.af

A numeric value specifying the threshold of major allele frequency for marker removal. Markers with major allele frequencies higher than this value will be removed. This value must be between 0 and 1.

Author(s)

Reiichiro Nakamichi

References

Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resources, 8, 103-106.

Examples

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# Example of GENEPOP file
data(data.JSM)
cat(data.JSM$MS.genepop, file="JSM_MS_genepop.txt", sep="\n")

# remove markers designated by their names
clip.genepop("JSM_MS_genepop.txt", "JSM_genepop_clipped_name.txt",
             remove.list=c("Sni21","Sni26"))

# remove markers with high major allele frequencies (in this example, > 0.5)
clip.genepop("JSM_MS_genepop.txt", "JSM_genepop_clipped_maf.txt",
             major.af=0.5)

# remove markers both by their names and by major allele frequencies
clip.genepop("JSM_MS_genepop.txt", "JSM_genepop_clipped_both.txt",
             remove.list=c("Sni21","Sni26"), major.af=0.5)


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