cepa.all.parallel | R Documentation |
use CePa package through parallel computing
cepa.all.parallel(dif = NULL, bk = NULL, mat = NULL, label = NULL,
pc, cen = default.centralities,
cen.name = sapply(cen, function(x) ifelse(mode(x) == "name", deparse(x), x)),
nlevel = "tvalue_abs", plevel = "mean", iter = 1000, ncores = 2)
dif |
differential gene list |
bk |
background gene list. If background gene list are not specified, use whole human genes |
mat |
expression matrix in which rows are genes and columns are samples |
label |
a |
pc |
a |
cen |
centrality measuments, it can ce a string, or a function |
cen.name |
centrality measurement names. By default it is parsed from |
nlevel |
node level transformation, should be one of "tvalue", "tvalue_sq", "tvalue_abs". Also self-defined functions are allowed, see |
plevel |
pathway level transformation, should be one of "max", "min", "median", "sum", "mean", "rank". Also, self-defined functions are allowed, see |
iter |
number of simulations |
ncores |
number of cores for parallel computing |
The function divides the pathway list into several parts and each part is sent to a core for parallel computing.
The package for parallel computing is snow
.
Note: there may be warnings saying connections not closed. In fact I have closed connections after the parallel computing is done. I don't know why this happens. Maybe you breaked the computing ahead manually. However it does not matter unless you have obsessive compulsive disorder.
A cepa.all
class object
Zuguang Gu <z.gu@dkfz.de>
Gu Z, Liu J, Cao K, Zhang J, Wang J. Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes. BMC Syst Biol. 2012 Jun 6;6(1):56.
cepa.all
## Not run:
data(PID.db)
# ORA extension
data(gene.list)
res.ora = cepa.all.parallel(dif = gene.list$dif, bk = gene.list$bk, pc = PID.db$NCI, ncores = 4)
# GSA extension
# P53_symbol.gct and P53_cls can be downloaded from
# http://mcube.nju.edu.cn/jwang/lab/soft/cepa/
eset = read.gct("http://mcube.nju.edu.cn/jwang/lab/soft/cepa/P53_symbol.gct")
label = read.cls("http://mcube.nju.edu.cn/jwang/lab/soft/cepa/P53.cls",
treatment="MUT", control="WT")
res.gsa = cepa.all.parallel(mat = eset, label = label, pc = PID.db$NCI, ncores = 4)
## End(Not run)
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