Step 6. Collect Information About the Current R Session.

Contact

The Centre for Artificial Intelligence Driven Drug Discovery (AIDD) at Macao Polytechnic University.

Location:

匯智樓 (WUI CHI)-4/F, N46B, Rua de Luís Gonzaga Gomes, Macau

Email:

kefengl@mpu.edu.mo

Call:

(+853) 8599 6883

Open Hours:

Mon-Fri: 10AM - 16PM


SNP Gene Mapping and Enrichment

MAGMA: Generalized Gene-Set Analysis of GWAS Data.

MAGMA is one the most commonly used tools for gene-based and gene-set analysis.

Click here for a demo:


MAGMA Introduction

MAGMA employs a multiple linear principal components regression, and F test to obtain P values for genes.

The workflow for performing MAGMA is as follows (See details):

  • Install MAGMA
  • Download reference files
  • Format input files
  • Annotate SNPs
  • Gene-based analysis
  • Gene-set level analysis

This application is conducted using MAGMA[1] (v1.10).

[1] de Leeuw CA, Mooij JM, Heskes T, Posthuma D. MAGMA: generalized gene-set analysis of GWAS data. PLoS Comput Biol. 2015 Apr 17;11(4):e1004219. doi: 10.1371/journal.pcbi.1004219. PMID: 25885710; PMCID: PMC4401657.

   Step 1. Choose SNP data.

No data selected! Use a data.frame from your environment or from the environment of a package.
No file selected: You can import .csv, .tsv, .txt, .bed, .xls, .xlsx, .gz files
[required] SNP, namely SNP ID in dbSNP databases, an it is an identifier for a SNP, which represents a specific variation in the genome.
[required] CHR indicates the chromosome on which the SNP is located in the genome (1, 2, 3, .., X, Y).
[required] POS denotes the position of the SNP on the chromosome.
[optional] P.VALUE is a statistical measure used to assess the assocaition between a SNP and a studied trait, such as a disease.
                     If this value is NULL, perform gene analysis on raw GWAS data. Otherwise, perform gene analysis on SNP P-values.

   Step 2. Gene Annotation.

   Step 3. Gene Analysis

   Step 4. Gene-set Analysis