Chunk #16 — DISCUSSION

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i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study.

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yes

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for LD since these can only be done when genotype data is available. So, users are recommended to input SNPs not in LD (say r2 < 0.2) to reduce the possibility of biased results due to LD patterns from SNP arrays. On the other hand, as the name of the web server defines, i-GSEA4GWAS is only applicable to whole-genome SNP arrays.