Question: How to analyze SNPs as variables?
0
gravatar for nayeona.hi
11 weeks ago by
nayeona.hi50
nayeona.hi50 wrote:

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 • 156 views
ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by nayeona.hi50

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 REPLYlink written 11 weeks ago by RamRS30k
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