Step 3 - gene p-values (common variants)

Step 3: obtaining gene-level p-values using the ACAT test

#check the help info for step 3
Rscript step3_gene_pvalue_qtl.R --help

–assocFile= is used to specify the step 2 output with single-variant association test results from step 2.

Rscript step3_gene_pvalue_qtl.R \
        --assocFile=./output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1_cis        \
        --geneName=gene_1       \
        --genePval_outputFile=./output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1_cis_genePval

Input files

(Required) assoc file from step 2

 less -S ./output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1_cis

(Optional) a file with weights for each single variant for the calculation of ACAT p-values.

The file has two columns: one with marker IDs that are used to match with MarkerID in the assocFile (output by step 2) and the other column contains weights used for each marker. The file needs to have a header with column names ‘MarkerID’ and ‘weight’. If not specified, equal weights will be used for all markers.

Output file

A file with gene-level p-value for the gene, top nominal p-value, and variant ID with the top nominal p-value
```
 less -S ./output/nindep_100_ncell_100_lambda_2_tauIntraSample_0.5_gene_1_cis_genePval
```