getAllele: Gets the allele code from an electrophoresis fragment size

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

Description

Rounds a fragment size with two decimal of a bp to an integer allele code

Usage

getAllele(fragRef, frag, limit)

Arguments

fragRef	A vector of fragments for a given locus
frag	A double, which is the fragment to be assigned to a bin
limit	Bin limits

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 iteger value

Value

An integer allele code

Author(s)

Kevin Keenan

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.loc

Examples

data(DBase)
fragRef <- DBase$Fragment[DBase$Marker == "BC-16"]
getAllele(fragRef, 142.54, 0.8)

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