getPCAFunc: Get principal components of arrays

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

Description

Get principal components of arrays.

Usage

getPCAFunc(es, 
           labelVariable = "subjID", 
            hybName = "Hybridization_Name",
           requireLog2 = TRUE,
           corFlag = FALSE
)

Arguments

es	An ExpressionSet object
labelVariable	A character string. The name of a phenotype data variable use to label the arrays in the boxplots. By default, labelVariable = "subjID" which is equivalent to labelVariable = "Hybridization_Name".
hybName	character string. indicating the phenotype variable Hybridization_Name.
requireLog2	logical. requiredLog2=TRUE indicates probe expression levels will be log2 transformed. Otherwise, no transformation will be performed.
corFlag	logical. Indicating if correlation matrix (corFlag=TRUE) or covariance (corFlag=FALSE) is used to obtain principal components.

Value

A list with 3 elements:

es.s	An ExpressionSet object with the arrays sorted according to Batch_Run_Date, Chip_Barcode, and Chip_Address
pcs	An object returned by the function prcomp of the R package stats. It contans the following components. sdev (the square roots of the eigenvalues of the covariance/correlation matrix); rotation (a matrix whose columns contain the eigenvectors); x (a matrix whose columns contain principal components); center (the centering used or FALSE); scale (the scale used or FALSE)
requireLog2	logical. The same value as the input requireLog2.

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)

    pca.obj = getPCAFunc(es = es.sim, 
               labelVariable = "subjID", 
               hybName = "memSubj",
               requireLog2 = FALSE,
               corFlag = FALSE
    )

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