Using PLINK to check SNP variation for a gene

Question

[ebrudermanver]

I have .bed, .bim and .fam files for the genetic information of some patients, and I also have the gene expression data from the relevant tissues for the same patients. I have some candidate genes that I want to check whether the expression variation in them is caused by some SNPs in the genetic data. I am familiar with gene expression data, but I have never used genetic data before. I read online that those .bed, .bim and .fam files are PLINK files, but I am really not sure if PLINK program can help me do what I want to do (checking the variation of the genetic content for a specific gene among the samples). Any ideas? Thanks.

[Floris Brenk]

I would avioid using plink for eQTL analysis. I would read and try out MatrixEQTL http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/

[vakul.mohanty]

As Floris said running eQTL analysis with plink isn't advisable. Instead I would suggest that you run MatrixEQTL, it is ridiculously fast and can handles additional covariates really well. You can also use PEER to identify hidden covariates for your expression data (https://github.com/PMBio/peer/wiki/Tutorial)