LumiBatch2Table {iCheck} | R Documentation |
Output slots (exprs, pData, fData) of an LumiBatch object into 3 text files.
LumiBatch2Table( es, probeID.var="ProbeID", gene.var="Symbol", chr.var="Chromosome", sep = ",", quote = FALSE, filePrefix = "test", fileExt = "csv")
es |
An LumiBatch object |
probeID.var |
character string. Name of the variable indicating probe ID in feature data set. |
gene.var |
character string. Name of the variable indicating gene symbol in feature data set. |
chr.var |
character string. Name of the variable indicating chromosome number in feature data set. |
sep |
Field delimiter for the output text files |
quote |
logical. Indicating if any character or factor. See also |
filePrefix |
Prefix of the names of the output files. |
fileExt |
File extension of the names of the output files. |
Suppose filePrefix="test"
and fileExt=".csv"
.
Then, the file names of the 3 output files are:
“test_exprs.csv”, “test_pDat.csv”,
and “test_fDat.csv”, respectively.
None.
Weiliang Qiu <stwxq@channing.harvard.edu>, Brandon Guo <brandowonder@gmail.com>, Christopher Anderson <christopheranderson84@gmail.com>, Barbara Klanderman <BKLANDERMAN@partners.org>, Vincent Carey <stvjc@channing.harvard.edu>, Benjamin Raby <rebar@channing.harvard.edu>
# generate simulated data set from conditional normal distribution set.seed(1234567) es.sim = genSimData.BayesNormal(nCpGs = 100, nCases = 20, nControls = 20, mu.n = -2, mu.c = 2, d0 = 20, s02 = 0.64, s02.c = 1.5, testPara = "var", outlierFlag = FALSE, eps = 1.0e-3, applier = lapply) print(es.sim) LumiBatch2Table( es = es.sim, probeID.var="probe", gene.var="gene", chr.var="chr", sep = ",", quote = FALSE, filePrefix = "test", fileExt = "csv")