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In the second method, referred to as the "unlinked method", selection coefficients were discerned without the inclusion of linkage, setting σ ˜ i e (t k ) = σ i for all time points.
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Thus, we limited the grant-to-article linkage set to those grants that have produced a minimum of four articles.
To increase completeness of a network model, all individual linkage sets inferred from different evidences are integrated based on the unified LLS.
The updated ranking score and the linkage set of each page are then passed as input to the next iteration.
In this paper, the MapReduce implementation of the PageRank algorithm proposed in [16] is modified as shown in Algorithm 2. The inputs of the map function are the page id p as the key, and its linkage set (N_{p}) and ranking score (R_{p}) as the value.
Positive and negative linkage sets were constructed from each of these reference sets as for the GO set.
To remedy this, the set of 720 k SNPs was reduced to a non-linkage disequilibrium set before linkage analysis by removing SNPs that exceed an R threshold of 0.1 and heterozygosity of >0.3.
We also employed two independent functional linkage reference sets for testing functional linkages.
The benefits of the divide-test-integrate method are illustrated in the improved precision for any given coverage of genes or reference linkages, as shown in Figure 3C on the independent MIPS protein functional linkage reference set (excluding the term "protein synthesis").
Log-likelihoods of the final integrated map order were computed with the RH and linkage data sets for comparison to the independent maps, using CarthaGene for the RH map and CRIMAP for the linkage map.
We have previously in a large T1D linkage data set demonstrated statistical evidence for gene-gene interactions [7].
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