processOpt: Preprocess a list of matrices for concordance analysis

In mengchen18/omic3plus: Different methods for the integrative analysis multiple omics data

Description

Internal function used to normalize a list of matrices passed into concordance analysis

Usage

processOpt(x, center = TRUE, scale = FALSE, option = c("lambda1",
  "inertia", "uniform", "nk"), value = 1, kx = NULL)

Arguments

x	a list of matrices to be preprocessed. The columns are variables and rows are observations
center	if the variables should be centered
scale	if the variables should be scaled
option	options for normalizing matrices, possible value are "lambda1", "inertia", "uniform", "nk"
value	Only used if option is "lambda1" or inertia, the matrix are weighted by value/lambda1
kx	used if option = "nk", normalize according to the number of kept variables (or inertia)

Value

a list of preprocess matrices has the same dimension as input x

Author(s)

Chen Meng

Examples

data("NCI60_4arrays")
dat <- lapply(NCI60_4arrays, t)
v <- processOpt(dat, option = "lambda1")

mengchen18/omic3plus documentation built on May 6, 2019, 4:59 p.m.