Description Usage Arguments Details Value Author(s) References See Also Examples
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 allele per column.
1 | write.PG.file.all(DB, refDB = DB, outfile = "Population genetics file.txt")
|
DB |
A data base of the type used by this package, like the generated by |
refDB |
A larger data set for optimal reference during the allele coding |
outfile |
A name for the output file |
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.
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 alleles. Alleles of a locus are given in two columns. 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
Filipe Alberto
Alberto F. MsatAllele_1.0: an R package to visualize the binning of microsatellite alleles Journal of Heredity. 100(3):394,397
write.PG.file.loc
, read.ah.file
1 2 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.