| uvSignif {mdgsa} | R Documentation |
Filters the rows in the data.frame returned by uvGsa
so that only the
enriched blocks are kept.
uvSignif(gsaout, cutoff = 0.05, pvalue = "padj", statistic = "lor", verbose = TRUE, sort = TRUE)
gsaout |
data.frame; output from uvGsa. |
cutoff |
p-value cutoff for considering significant a Gene Set. |
pvalue |
p-value column to be used. Default is named "padj" as in uvGsa output. |
statistic |
name of the column containing the log odds ratio from the uvGsa analysis. |
verbose |
verbose |
sort |
if TRUE the output data.frame is ordered according to significance. |
Works as goLeaves but without removing redundant terms.
The input data.frame but keeping just the 'significant' functional blocks.
David Montaner dmontaner@cipf.es
uvGsa, uvPat,
propagateGO, pval2index, goLeaves
uvGsa.res <- as.data.frame (list (N = c (10, 20, 30, 40),
lor = c (1.45, -0.32, 1.89, -1.66),
pval = c (0.001, 0.002, 0.05, 0.06)))
uvGsa.res[,"padj"] <- p.adjust (uvGsa.res$pval, "BY")
uvGsa.res
uvSignif (uvGsa.res)
## Not run:
res <- uvGsa (rindex, annotList)
uvSignif (res)
## End(Not run)