NA's in summary output

[tmajaria]

Currently, if there are any pvalues == NA in the raw results files, an equal number of NA rows will be produced in the top results output from the summarization task. This is due to filtering over the pvalue column, comparing NA to a scaler (line 223 of summarize_GWAS.R).

The fix should be:

top.assoc <- assoc[!is.na(assoc[,pval]),]
top.assoc <- assoc[assoc[,pval] < pval.threshold, ]