quipu-package: Quipu-type charts for a set of SSR markers.
In quipu: Summary charts of micro satellite profiles for a set of biological samples
Description
The chart shows SSR marker weights on a linear scale where
each allele or 'gel band' is represented by a circle. The
circle's diameter is sized inversely by its rareness within
the set of accessions in the database at hand and within
that locus. The purpose is to facilitate the visual
screening and comparison of genotypes with regard to these
two questions:
Details
What is the overall pattern of alleles in a genotype?
Which genotypes have rare alleles?
Motivation: Genebanks increasingly use molecular markers
for routine characterization of ex-situ collections and
farmer managed diversity. CIP's (International Potato
Center) genebank presently uses a SSR marker-kit to produce
molecular profiles for potato accessions. We have been
searching for a compact graphical representation that shows
both molecular diversity and accession characteristics -
thus permitting biologists and collection curators to have
a simpler way to interpret high-volume data. Inspired by
the ancient Andean quipus we devised a graph that allows
for standardized representation while leaving room for
updates of the marker kit and the collection of accessions.
The graph has been used in several CIP publications.
quipu documentation built on May 29, 2017, 2:47 p.m.
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Description
The chart shows SSR marker weights on a linear scale where each allele or 'gel band' is represented by a circle. The circle's diameter is sized inversely by its rareness within the set of accessions in the database at hand and within that locus. The purpose is to facilitate the visual screening and comparison of genotypes with regard to these two questions:
Details
What is the overall pattern of alleles in a genotype?
Which genotypes have rare alleles?
Motivation: Genebanks increasingly use molecular markers for routine characterization of ex-situ collections and farmer managed diversity. CIP's (International Potato Center) genebank presently uses a SSR marker-kit to produce molecular profiles for potato accessions. We have been searching for a compact graphical representation that shows both molecular diversity and accession characteristics - thus permitting biologists and collection curators to have a simpler way to interpret high-volume data. Inspired by the ancient Andean quipus we devised a graph that allows for standardized representation while leaving room for updates of the marker kit and the collection of accessions. The graph has been used in several CIP publications.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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