iCheck (version 1.2.0)

LumiBatch2Table: Output slots (exprs, pData, fData) of an LumiBatch object into 3 text files

Description

Output slots (exprs, pData, fData) of an LumiBatch object into 3 text files.

Usage

LumiBatch2Table( es,  probeID.var="ProbeID", gene.var="Symbol", chr.var="Chromosome", sep = ",",  quote = FALSE, filePrefix = "test",  fileExt = "csv")

Arguments

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 write.table.

filePrefix

Prefix of the names of the output files.

fileExt

File extension of the names of the output files.

Value

None.

Details

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.

Examples

    # 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")