Method Description:
Often in human genetic analysis, multiple tables of single SNP statistics
are shown alongside a Haploview-style correlation plot. Readers are then
asked to make inferences that incorporate knowledge across these multiple
sets of results. To better facilitate a collective understanding of all
available data, we developed a Ruby application, LD-Plus, that
simultaneously displays physical location of SNPs, simple genomic
annotation, binary SNP attributes (such as coding/non-coding or inclusion on
genotyping platforms), common haplotypes and their frequencies, and
continuously scaled values (such as Fst, minor allele frequency, genotyping
efficiency, or p-values), all in the context of the D' and r2 linkage
disequilibrium structures. Combining these results into one comprehensive
figure reduces dereferencing between figures and tables, and can provide
unique insights into genetic features that are not clearly seen when results
are partitioned across multiple figures and tables.
Software:
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