sortExpressionSet: Sort the order of samples for an ExpressionSet object

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

Description

Sort the order of samples for an ExpressionSet object.

Usage

sortExpressionSet(
    es, 
    varSort = c("Batch_Run_Date", "Chip_Barcode", "Chip_Address"), 
    timeFormat = c("%m/%d/%Y", NA, NA)
)

Arguments

es	An ExpressionSet.
varSort	A vector of phenotype variable names to be used to sort the samples of es.
timeFormat	A vector of time format for the possible time variables in varSort. The length of timeFormat should be the same as that of varSort. For non-time variable, the corresponding time format should be set to be equal to NA. Please refer to function strptime of the base package.

Value

An ExpressionSet object with samples sorted based on the variables indicated in varSort.

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)

  es.sim$Batch_Run_Date = 1:ncol(es.sim)
  es.sim$Chip_Barcode = 1:ncol(es.sim)
  es.sim$Chip_Address = 1:ncol(es.sim)
  

  es.sim2 = sortExpressionSet(
    es = es.sim, 
    varSort = c("Batch_Run_Date", "Chip_Barcode", "Chip_Address"), 
    timeFormat = c("%m/%d/%Y", NA, NA)
  )
  

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