How to analyze SNPs as variables?
0
0
Entering edit mode
4.3 years ago
nayeona.hi ▴ 60

Hi, this may be the silly question, and please understand.

I'd like to know the SNPs related to personalities influencing on a specific disease.
such as: rs3814424 (conscientiousness)
rs57590327 (extraversion)
rs2164273 (extraversion)
rs6481128 (extraversion)
(https://www.snpedia.com/index.php/Personality)

I got a bim file from MAP and PED files.
Through the data, I have the matching SNPs.
For example,

df = pd.DataFrame({'CHR': [10, 8, 3], 'RS_ID': ['rs3814424', 'rs57590327', 'rs2164273'], 
                   'MORGAN':[1, 1, 1],  'BP_Position': [20466206, 58220209, 8262926], 
                   'allele A' : ['C', 'C', 'T'], 'allele B': ['T', 'A', 'C']}, 
                  columns = ['CHR', 'RS_ID', 'MORGAN', 'BP_Position', 'allele A', 'allele B'])

df

ab

I think I have to get the individuals(samples) information from a MAP file,
especially matching the above SNPs.

How can I get the information?
Do I have to use plink? please let me know the method. Thank you.

SNP model • 883 views
ADD COMMENT
0
Entering edit mode

Does SNPedia offer data downloads or APIs for query? If so, this is a straightforward task. I can't wrap my head around that website.

ADD REPLY

Login before adding your answer.

Traffic: 1807 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6