Logistic Regression Using Plink Files
1
0
Entering edit mode
7.7 years ago
madieke • 0

Hi All,

I am trying to determine the relative effect size of a set of variants using logistic regression (in R?). I have plink files to start from. Since this is a pretty common problem I was wondering if there is a straightforward R pipeline to do this. I searched around but so far no luck.

Thank you for any leads. General leads for good packages to analyze plink files in R also highly appreciated! Thanks!

plink r • 2.4k views
ADD COMMENT
0
Entering edit mode

Why not use plink --logistic?

ADD REPLY
0
Entering edit mode

Thank for your reply. I have tried plink's --logistic, but I dont think I am able to calculate nagelkerke's R^2 using plink. I may be mistaken though, and I am looking into this more now. Thanks again!

ADD REPLY
0
Entering edit mode
7.6 years ago
Ahill ★ 1.9k

For simple access to analyze non-huge .bed or .ped data in R, try plink --recode options, such as

cmd <- "plink --bfile UC_N10_M5_P1_C1 --recodeAD --out plink"
system(cmd)
res <- read.table("plink.raw", header=TRUE)

For more details read the manual.

Another option apparently exists to extend PLINK with RSERV (I've never used it). Especially for large datasets it will be faster/easier to use plink directly for any analyses where that is possible, instead of transferring data into R (as suggested by zx8754).

ADD COMMENT

Login before adding your answer.

Traffic: 2506 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