Missing value filter hinders advanced users access complete GSEA result

[hsiaoyi0504]

Both GSEA method currently filter out terms with missing values in p-value column.

DOSE/R/gsea.R

Line 88 in 1ce3c6f

res <- res[!is.na(res$pvalue),]

DOSE/R/gsea.R

Line 324 in 1ce3c6f

res <- res[!is.na(res$pvalue),]

This might not be ideal since cases with unbalanced gene-level statistic values, pval, padj, NES, log2err are set to NA, which further prevent users that would like to view the complete results without any cutoffs by setting pValueCutoff=1. Could we have a separate argument like reportNA to ensure advanced users could access the results?

5: In fgseaMultilevel(pathways = pathways, stats = stats,  ... :
  There were 2 pathways for which P-values were not calculated properly due to unbalanced (positive and negative) gene-level statistic values. For such pathways pval, padj, NES, log2err are set to NA. You can try to increase the value of the argument nPermSimple (for example set it nPermSimple = 10000)

[hsiaoyi0504]

Additionally, when such cases happened when by="DOSE", no any warning messages will be shown.