p.table | R Documentation |
Table of p-values of pathways
p.table(x, adj.method = NA, cutoff = ifelse(adj.method == "none", 0.01, 0.05))
x |
a |
adj.method |
methods in |
cutoff |
cutoff for significance |
Since the p-values for each pathway are calculated for several centralities, the whole p-values are represented as a table.
Also it can extract significant pathways only.
A data matrix where rows are pathways and columns are centralities.
Zuguang Gu <z.gu@dkfz.de>
cepa.all
## Not run: data(PID.db) # ORA extension data(gene.list) # will spend about 20 min res.ora = cepa.all(dif = gene.list$dif, bk = gene.list$bk, pc = PID.db$NCI) p.table(res.ora) p.table(res.ora, adj.method = "BH") # GSA extension # P53_symbol.gct and P53_cls can be downloaded from # http://mcube.nju.edu.cn/jwang/lab/soft/cepa/ eset = read.gct("P53_symbol.gct") label = read.cls("P53.cls", treatment="MUT", control="WT") # will spend about 45 min res.gsa = cepa.all(mat = eset, label = label, pc = PID.db$NCI) p.table(res.gsa) ## End(Not run)
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