Plink: How do I run an association analysis?

Question

[melissachua90]

First, I filtered out SNPs and subjects and then performed MDS analysis.

./plink --file subjects_153 --maf 0.1 --geno 0.1 --mind 0.3 --hwe 0.001 --recode

    ./plink --noweb --file filtered --genome --out filtered
    ./plink --cluster --file filtered --mds-plot 2 --noweb --out filtered --read-genome filtered.genome

Now, I want to run an association analysis using linear regression to identify SNPs associated with bipolar disorder (compare bipolar subjects to the control subjects). I also want to include information regarding primary eigenvector from the MDS calculation, Gender, and Left Brain (fixed/frozen). I want to report the disease status in a separate file).

Essentially, I want to create 3 files:

• subjects to keep for the study (--keep)
• covariates (--covar)
• affected status (--pheno)

`d <- read.table("filtered.mds", header=T)
ann <- read.table("clinical_table.txt", header=T, sep="\t")`


 `# Add hyphens to the Family IDs
 d$FID <- sub("(\\D)(\\d)", "\\1-\\2", d$FID)
ann$Database_ID <- d$FID`

`dat <- as.data.frame(cbind(ann$Profile, d$C1, d$C2))`

`library(data.table)
fwrite(dat, "mycov.txt", sep="\t")`

`./plink --noweb --ped filtered.ped --map filtered.map --logistic --covar mycov.txt
./plink --file filtered --make-bed`

`pheno <- read.table("plink.fam", header=T)
fwrite(pheno, "pheno.txt", sep="\t"`

`library(dplyr)
bdf <- d %>% semi_join(ann %>% filter(Profile=="BP"||Profile==”Unaffected control”), by=c("FID"="Database_ID"))
fwrite(bdf, "keep.txt", sep="\t")
./plink --file plink.fam --keep keep.txt`

Traceback:

Error: Basic file conversions do not support regular filtering operations. Rerun your command with --make-bed.