Table 1. Overview of Crohn’s Disease analyses.
| Name | Analysis | Input | Settings |
|---|---|---|---|
| MAGMA-main | gene, self-cont., comp. | Raw data | Multiple regression model (per gene) |
| MAGMA-mean | gene | Raw data | Mean SNP χ 2 (per gene) |
| MAGMA-top | gene | Raw data | Top SNP χ 2 (per gene) |
| MAGMA-pval | gene | SNP p-values, HapMap data | Mean SNP χ 2 (per gene) |
| MAGMA-pval-1K | gene, self-cont., comp. | SNP p-values, 1,000 Genomes data | Mean SNP χ 2 (per gene) |
| VEGAS | gene | SNP p-values, HapMap data | Mean SNP χ 2 (per gene) |
| PLINK-avg | gene, self-contained | Raw data | Mean SNP χ 2 |
| PLINK-prune | gene, self-contained | Raw data | Mean SNP χ 2, SNP pruning |
| PLINK-top | gene | Raw data | Top SNP χ 2 |
| ALIGATOR | competitive | SNP p-values | 4 SNP p-value cut-offs |
| INRICH | competitive | SNP p-values | 4 SNP p-value cut-offs |
| MAGENTA | competitive | SNP p-values | 2 gene score quantile cut-offs |