readInputFile: Read the input data and creating the data structures

In haimbar/SEMMS: Variable selection in Generalized Linear Models - an empirical Bayes approach

Description

Read a text file containing the response variable, any fixed effects (possibly none), and the putative variables. An intercept does not have to be in the data file - it can be added by this function. The function can also add all two-way interactions. The data may be loaded from an RData file, if is has been stored in the format that this function generates. The interaction terms are transformed using the scale function.

Usage

readInputFile(
  file,
  skip = 0,
  header = TRUE,
  sep = "\t",
  ycol,
  Zcols,
  Xcols = c(),
  addIntercept = TRUE,
  logTransform = c(),
  twoWay = FALSE
)

Arguments

file	The input file name.
skip	How many lines to skip in the input file (default=0).
header	Does the first line being read contain column names? (default=TRUE).
sep	The delimiter (default is \t).
ycol	The number of the column in the input file which should be used as the response.
Zcols	The columns in the input file which contain the putative variables.
Xcols	The columns in the input file which contain the fixed effects in the model (default is none, c()).
addIntercept	Whether to add an intercept column to the fixed effects (default=TRUE).
logTransform	The column numbers which have to be log-transformed (default is none, c()).
twoWay	Whether to add all two-way interactions to the putative variables (default=FALSE).

Value

Z	A numeric matrix of putative variables (the columns of Z)
Y	The response vector
X	Fixed effects matrix (could be null)
originalZnames	The original names of the columns of the matrix Z
colnamesZ	The generated column names, Z0001, Z0002, etc.
N	The number of samples, nrow(Z)
K	The number of putative variables, ncol(Z)
P	The number of fixed effects, ncol(X)

Examples

## Not run: 
fn <- system.file("extdata", "ozone.txt", package = "SEMMS", mustWork = TRUE)
dataYXZ <- readInputFile(fn, ycol=2, Zcols=3:11,
addIntercept = TRUE, logTransform = 2, twoWay = TRUE)
## End(Not run)

haimbar/SEMMS documentation built on Dec. 20, 2021, 2:44 p.m.