write.PG.file.loc: Writes a file with the bin codes with one column per locus

In kkeenan02/MsatAllele: Visualizes the scoring and binning of microsatellite fragment sizes

Description

Writes a file in the working directory. Uses the information on the database to write a file in the appropriate format for most population genetics analysis software. The output format has one locus per column.

Usage

write.PG.file.loc(DB, refDB = DB, outfile = "Population genetics file.txt")

Arguments

DB	A data base of the type used by this package, like the generated by transDB function
refDB	A larger data set for optimal reference during the allele coding
outfile	A name for the output file

Details

The algorithm implemented searchs the database for all observed fragments within the interval set by -0.8 to + 0.8 bp of the fragment. It proceeds to detect breaks in the distribution of observed distribution to find the distribution where the fragment belongs. To get the allele code the median of that distribution is rounded to an integer value.

Value

A table is written into the working directory (.PG.txt file) with the first column having the sample names and every subsquent column the information for the loci. Both alleles of a locus are given in the same column (i.e. one column per locus). There is also a file written with the counts for the number of fragments for each combination of locus and sample (AC.txt file), remember that there should be only a maximum of 2 for this value, otherwise the code will write the first two fragments scored to build the genotype

Author(s)

Filipe Alberto

References

Alberto F. MsatAllele_1.0: an R package to visualize the binning of microsatellite alleles Journal of Heredity. 100(3):394,397

See Also

write.PG.file.all, read.ah.file

Examples

data(DBase)
	write.PG.file.loc(DBase)

kkeenan02/MsatAllele documentation built on May 20, 2019, 10:42 a.m.