Consistent Form Design

Type your GeneSet ID from GeneWeaver.

Avoid adding spaces around the commas when entering each GeneSet.

For example, you can type the Gene Set IDs: 399058,399061,1777 in the text box.

GeneSet Labels

Avoid adding spaces around the commas when entering each GeneSet labels.

For example, if you enter 75605 and 407736, label them as Alcoholic_Frontal_Cortex and Alcohol_Gene_Expression_Mice. Use underscores (_) instead of spaces and separate each label with a comma.

Upload Your GWAS

Download example GWAS datasets here: Example!

GWAS Sample Size

Window Size (Buffer Region)

Note: The window size ranges from 100 to 100,000. For 10K, enter 10000.

Input Format

Geneset Upload

Here’s an example of a correctly formatted geneset upload file:

ENSMUSG00000026842

ENSMUSG00000026003

ENSMUSG00000029545

ENSMUSG00000023328

ENSMUSG00000028405

ENSMUSG00000026836

Instructions for Preparing Your Summary Statistics File

1. Format Your Summary Statistics File:

Upload your GWAS file in a compressed .gz format.
Ensure the file includes the required columns: SNP_ID, CHR, POS, A1, A2, Beta, SE, and Pval.
A1 should represent the effect allele.
If your data only includes Z-scores instead of Beta and standard error, you need to convert them. Refer to the following resources for guidance:
- Link 1
- Link 2

2. Provide Sample Size:

Include the overall sample size reported in the manuscript for polygenic score (PGS) calculations.

3. Include Chromosome and Position Information:

If your file lacks chromosome and position details, features like the Manhattan plot and PGS functionality will not work.
To map RS IDs to chromosome and position, use the following tool: GitHub Repository: Map_RSID

4. Compress the File to `.gz` Format:

After preparing your GWAS file, you need to compress it to a .gz format before uploading.
Here are two options for compressing your file:

Option 1: Using R:

		library(R.utils)

		write.table(test_dat, file = "test_dat_R.txt", sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE)
		gzip("test_dat_R.txt", destname = "test_dat_R.gz", overwrite = TRUE)

Option 2: Using Windows:
- You can use a compression tool like 7-Zip or the built-in Compress to .gz feature in Windows.
- To use 7-Zip, right-click the file and choose 7-Zip > Add to archive..., then select .gz as the archive format.

Here’s an example of a correctly formatted input file:

SNP_ID	CHR	POS	A1	A2	Beta	SE	Pval
rs11130222	3	49901060	A	T	0.026	0.003	4.581e-25
rs2883059	3	49902160	T	C	0.026	0.003	7.149e-25
rs3796386	3	49899795	A	G	-0.026	0.003	8.883e-25
rs55692411	3	49911155	A	G	-0.026	0.002	1.045e-24
rs952594	3	49908023	A	G	-0.026	0.002	1.291e-24
rs34654589	3	49911449	C	G	0.026	0.002	1.549e-24

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