Description Usage Arguments Value
Preprocess input data with Principal Component Analysis method (PCA)
1 2 3  preprocess(data, pheno = NULL, method = "pca", reg.family = "binomial",
scaleData = FALSE, cumvar.threshold = 75, out.type = "D",
penalty = 0.001, verbose = FALSE)

data 
An input matrix with values of independent variables (predictors). 
pheno 
A phenotype  columnvector, needed for LASSO/ridge and

method 
A dimensionality reduction method.
Default: 
reg.family 
A regression family.
Default: 
scaleData 
A logical variable, indicates wheither or
not scaling should be performed. Default: 
cumvar.threshold 
A threshold value for explained variance.
Default: 
out.type 
An output (phenotype) type.
Default: 
penalty 
Value of penalty parameter for LASSO/ridge regression.
Default: 
verbose 
Indicates verbosing output. Default: FALSE. 
A list of one: "S"  a data frame of predictor values.
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