everyone!
I am trying to run a GWAS analysis in R on some very simple genetic data. It only contains the SNPs and one outcome variable (as well as an ID variable for each observation).
Everything I have found online includes chromosome and position data. I have that for the SNPs, but in a separate file. (My plan is to map the SNPs after the relevant ones have been selected).
How can I go about running a GWAS analysis on this data? Would I need to, or could I use another method to filter to only the most significant SNPs?
I tried this, but it didn't work, because my data is not a gData object.
# SNPs are in A/B notation, with 0 = AA, 1 = AB, and 2 = BB
library(statgenGWAS)
id <- c("person1", "person2", "person3", "person4", "person5", "person6", "person7", "person8", "person9", "person10")
snp1 <- c(0, 1, 2, 2, 1, 0, 0, 0, 1, 1)
snp2 <- c(2, 2, 2, 1, 1, 1, 0, 0, 0, 1)
snp3 <- c(0, 0, 2, 2, 0, 2, 1, 0, 2, 2)
diagnosis <- c(0, 1, 1, 0, 0, 1, 1, 0, 1, 1)
data <- as.data.frame(cbind(id, snp1, snp2, snp3, diagnosis))
gwas1a <- runSingleTraitGwas(gData = data,
traits = "diagnosis")
Any help here is appreciated.
Thank you!