Understanding dbGaP study analysis table
I was looking for datasets in dbGap and found some publicly available analysis results. For example, analysis of this cancer ftp://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs001263/analyses/phs001263.pha004499.txt
This analysis has following columns
SNP ID Marker Type P-value Chr ID Chr Position Rank Allele1 Allele2 Sample size Effect Allele Odds ratio CI low CI high Bin ID
What I am looking for is the meaning of the columns, specially the important columns like p-value. I looked in the dbgap website, but could not find the meaning or explanation of each columns. It would be great help for people from different study background. Thanks in advance.
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From the link you provided, it says 'testing' p value, whatever testing means. The lower the value, the more significant is the association. But you need to check with the original resource (or authors) for more details. It seems the method for analyses is from the METAL software package. So I guess their wiki will give some info on the statistical analyses.