Input file format - Githubissues

StoreyLab / qvalue

R package to estimate q-values and false discovery rate quantities.

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Input file format #13

Closed TinaNeik closed 5 years ago

TinaNeik commented 6 years ago

Hi,

I have a set of 27577 p-values obtained from GWAS MLM Q + K in TASSEL. I want to perform FDR on these p-values using qvalue package in R. May I ask, what is the input data format? I opened the data "hedenfalk" in R but don't understand how is it formatted. Could you please help me?

Thank you.

ajbass commented 5 years ago

The qvalue function requires a vector of p-values. You can access the p-values from the hedenfalk example as

pvals <- hedenfalk$p