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

In FinePop2: Fine-Scale Population Analysis (Rewrite for Gene-Trait-Environment Interaction Analysis)

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

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

# Example of GENEPOP file
data(jsmackerel)
jsm.genepop.file <- tempfile()
cat(jsmackerel$MS.genepop, file=jsm.genepop.file, sep="\n")

# Remove markers designated by their names
clipped_by_name.jsm.genepop.file <- tempfile()
clip.GENEPOP(infile=jsm.genepop.file,
             outfile=clipped_by_name.jsm.genepop.file,
             remove.list=c("Sni21","Sni26"))

# Remove markers with high major allele frequencies (in this example, > 0.5)
clipped_by_af.jsm.genepop.file <- tempfile()
clip.GENEPOP(infile=jsm.genepop.file,
             outfile=clipped_by_af.jsm.genepop.file,
             major.af=0.5)

# Remove markers both by their names and by major allele frequencies
clipped_by_both.jsm.genepop.file <- tempfile()
clip.GENEPOP(infile=jsm.genepop.file,
             outfile=clipped_by_both.jsm.genepop.file,
             remove.list=c("Sni21","Sni26"), major.af=0.5)

# See four text files in temporary directory.
#  jsm.genepop.file                 : original data of five markers
#  clipped_by_name.jsm.genepop.file : clipped data by marker names
#  clipped_by_af.jsm.genepop.file   : clipped data by allele frequency
#  clipped_by_both.jsm.genepop.file : clipped data by both names and frequency

FinePop2 documentation built on March 26, 2020, 9:01 p.m.