We therefore checked cluster plots for all core SNPs that showed significant associations.
As this SNP was imputed in all studies driving the association, we checked cluster plots of all directly typed variants 500 kb upstream and downstream of the associated SNP in all studies, excluded SNPs with poor clustering, re-imputed the region and re-run the meta-analysis.
We, therefore, systematically checked clustered distorted SNP markers from the 12 k assay in a larger sample (380 F2s) with a targeted medium-throughput genotyping assay (Mass Array, Sequenom).
This module includes functions responsible for checking the cluster status and terminating the cluster.
Preliminary identification of clusters of orthologs of RR and HK sequences was performed by creating an orthology table of the 19 genomes used in this study using the clustering algorithm implemented in MBGD [ 43] and manually checking the clusters of orthologs thus obtained for each previously identified TCS gene.
Based on the SOM based spectral clustering described in previous section and the current LPIS, the method first finds a land cover mapping (with a predetermined number of clusters) in an unsupervised manner, then constructs an eligibility mask by checking whether clusters are eligible or ineligible according to the current LPIS.
This will be corrected for by using socio-economic characteristics of the patients (e.g. education), demographic factors (e.g. age and marital status) and by checking for clustering at the regional level in the multilevel analysis.
Intervention effects were determined by one-way analysis of covariance and logistic regression, after checking for clustering effects of school, and moderating effects of gender, pubertal status and parental education.
Since there is an assumed clustering given that the study participants were sampled from specific health facilities (i.e. 33 clusters), we checked for clustering effect by use of an Intraclass Correlation (ICC) [ 38– 40].
The routing from S to G1 is performed within the cluster by checking the intra-cluster routing tables.
A P-value is calculated using the one-tailed Fisher's exact test to assess whether N AC /N C > N AI /N I and annotation term A is enriched in cluster C. Such functionality is very useful to check the cluster quality at different identity levels and also for function assignment of proteins with unknown function.
