Data Input

The following are the links for the example dataset used in the GIFT.

Simulation #

GIFT: Using individual-level data as input: #

Different genotype data formats:

• plink binary (.bim/.fam./.bed)
• vcf
• ped/map
• csv
• tsv

Other dataset:

• individual_data.Rdata

GIFT: Using summary statistics as input: #

Different summary statistics data formats:

• plink binary (.bim/.fam./.bed)
• GEMMA
• SAIGE

Different LD matrix data formats:

• matrix format from eQTL data
• matrix format from GWAS data
• long format from eQTL data (.h5)
• long format from GWAS data (.h5)

Other dataset:

• SNP list
• estimated correlated matrix of gene expressions
• LD matrix from 1,000 Genomes project

Two-stage version of GIFT: Using pre-trained weights and summary statistics as input: #

eQTL weight:

• the BLUP weight

Different summary statistics data formats:

• plink binary (.bim/.fam./.bed)
• GEMMA
• SAIGE

For the visualization: #

• TWAS result

Real data application #

• realdata.RData