LumiBatch2Table: Output slots (exprs, pData, fData) of an LumiBatch object...

In iCheck: QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data

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.

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.

Value

None.

Author(s)

Weiliang Qiu <[e-mail]>, Brandon Guo <[e-mail]>, Christopher Anderson <[e-mail]>, Barbara Klanderman <[e-mail]>, Vincent Carey <[e-mail]>, Benjamin Raby <[e-mail]>

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")

iCheck documentation built on Nov. 8, 2020, 11:09 p.m.