LDna: Linkage disequilibrium network analyses (LDna)

In petrikemppainen/LDna: Linkage disequilibrum network analysis (LDna)

Linkage disequilibrium network analyses (LDna)

Description

Linkage disequilibrium network anlysis (LDna) is an exploratory tool for population genomic data that based on pairwise LD values can be used to identify and extract sets of loci that bear distinct population genetic signals.

Details

The main pipeline is to produce raw data using: LDnaRaw, extract clusters using: extractBranches, summerise data using: summaryLDna and exploring networks using plotLDnetwork.

Since LDna considers all pairwise LD-values in a matrix it is not practical for more than 10-20k SNPs at a time (and need a lot of RAM). LDna can therefore be performed in a nested fashion starting by finding LD-clusters within windows within chromosomes using LDnClusteringEL. Edge lists of LD-values need to be provided by the user though.

Author(s)

Petri Kemppainen, [e-mail] and Christopher Knight Christopher Knight, [e-mail]

See Also

Useful links:

• http://www.github.com/petrikemppainen/LDna

petrikemppainen/LDna documentation built on April 14, 2024, 6:37 p.m.