Haplotype blocks were selected with Haploview software by considering linkage disequilibrium (LD) blocks.
In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium.
Considering linkage disequilibria of alleles in haplotypes, HLA-A11-B27-Cw12 was the most common haplotype in both bamboo and non-bamboo groups (95.23% vs. 91.22%, respectively, P = 0.238).
The researchers on the project noted that when considering linkage disequilibrium (LD), there are approximately one million independent loci in the human genome (α = 5 × 10−8 is the Bonferonni-corrected threshold for a million tests).
See http://www.workcover.com/ The inclusion of data sets unrelated to health was deemed important, as this provided a contrasting effect bringing to the fore issues people considered pertinent when considering linkage of health data alone, compared to health and other data.
To identify functional modules regulated by RFX2 in unbiased way, we clustered this network using the clusterONE algorithm (Nepusz et al., 2012) available in Cytoscape (version 2.8.3) (Shannon et al., 2003; Cline et al., 2007), considering linkage confidence scores during the clustering.
Future studies may consider linkages with additional data sources.
The functional analysis implemented in our web server for SNPs in trait-associated pathways considers linkage disequilibrium (LD) information, three categories of features (coding, non-coding and eQTLs) and enrichment analysis, which is a very comprehensive tool/module in comparison to available web-based tools for functional analysis (Table S6).
For these simulations, we considered linkage studies of 100 families, each family consisting of 2 parents and 2 offspring.
Since linkage effects may extend up to 20 cM [28], we also considered linkage results within 20 cM of previously characterized candidate genes as possible replications.
