Hi everyone!
I have 170 samples. For each sample I have a vcf file with the SNPs and an other file with values corresponding to Drug sensitivity values for 500 drugs.
The final files are:
File2:
FID IID/Drug Drug1 Drug2 Drug3. ..... Drug500 0 Sample1 0.8 0.4 ........ ...... 0.9 0 Sample2 0.3 -9 ........... ........... 0.3 . . . 0 Sample170
and the merged vcf file for all samples
FIle1 (vcf):
Chr Pos ... Sample1 Sample2 ... Sample170 1 1 1 . . . . . Y
Can you help me on how to make association between specific SNPs and the abberations (changes) in drug sensitivity of a particular drug?
Do I have to use a command like this? Is this right? Have you other suggestions?
plink --vcf-half-call r --const-fid 0 --vcf MERGED.vcf.gz --pheno DrugSensitivityAnalysisFinal.tsv --allow-no-sex --all-pheno --linear --pfilter 5e-4 --ouT results
