Question: How to find the association between SNP and multiple traits or diseases
0
gravatar for wtvxy
2.5 years ago by
wtvxy0
wtvxy0 wrote:

A disease may relate to multiple traits or diseases which means multiple traits may cause a disease. Now I have a data of 10 related traits of 10 column, 1 represent a sample have this trait, 0 represent doesn't have. Each row represents a sample.

A 6 samples examlpe:

0 0 0 0 0 0 0 0 0 0

1 0 0 1 0 0 0 0 0 0

1 1 1 1 0 0 0 1 1 1

0 1 1 1 0 1 0 0 0 0

1 1 1 1 1 1 1 1 1 1

Each sample has many SNPS:

3 2 1 2 1 1 1 1 1 1 1

2 2 2 2 3 2 1 1 1 1 1

3 3 1 1 3 2 3 1 1 1 1

3 1 1 2 2 1 2 2 2 2 2

2 2 2 3 2 1 2 1 3 1 2

2 1 1 2 1 1 1 1 3 3 1

The question is: How can I find the relation between SNPs and traits?

In this question,the disease/trait label more than one dimension.

Which algorithm should I use?

snp gene genome • 703 views
ADD COMMENTlink modified 2.5 years ago by chrishengbee20 • written 2.5 years ago by wtvxy0
0
gravatar for vakul.mohanty
2.5 years ago by
vakul.mohanty240
United States
vakul.mohanty240 wrote:

You could build a linear regression model between the trait and the genotype. Yo can add covariates to the model to account for confounding factors. You can use tools like plink or MatrixEQTL to carry out the analysis

ADD COMMENTlink written 2.5 years ago by vakul.mohanty240
0
gravatar for chrishengbee
2.5 years ago by
chrishengbee20
chrishengbee20 wrote:

Hi,guy! Guess u are doing modeling competition ha? It's the last night. Good luck for u!

ADD COMMENTlink written 2.5 years ago by chrishengbee20
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