GWAS analysis with logistic regression in R

Question

[a.elriedy]

hi, I got this Excel file (example below) with 191 SNPsHotspot.ID) and 201 subjects(EK...), and I would like to put it in a format or rearrange it, so it would be suitable to run logistic regression (or lasso) in R on it. So how do u think the data should be arranged so i can run a logistic regression model on it. And is there are any packages that i can feed it this excel sheet directly?

ID           Cohort Sex        HotSpot.ID       Genotype    Allele.1    Allele.2
EK001   normal  female  rs1037715   CT      C              T
EK001   normal  female  rs1042173   AA      A              A 
EK001   normal  female  rs1051730   AG      A              G
EK001   normal  female  Promotor    SL      S              L
EK001   normal  female  rs1042114   TT      T              T
EK001   normal  female  rs678849    TT      T              T
EK001   normal  female  rs2298896   TT      T              T
EK001   normal  female  rs12749204  AA      A              A
EK001   normal  female  rs2234918   CT      C              T
EK001   normal  female  rs204076    AT      A              T
EK001   normal  female  rs1506700   TT      T              T
EK001   normal  female  rs3121147   TT      T              T
EK001   normal  female  rs1344694   GG      G              G

Answer 1

[mastal511]

If you save the excel worksheet as a delimited .txt file, you can read it into R with read.table(), and then you can have it as a data.frame or matrix. As for what format to use with lasso, you would have to read the lasso documentation to find out.