getCanWeightsMulti {SmCCNet}

Get Canonical Weight SmCCA Algorithm (No Subsampling)

Description

Run Sparse multiple Canonical Correlation Analysis (SmCCA) and return canonical weight vectors.

Usage

getCanWeightsMulti(
  X,
  Trait = NULL,
  Lambda,
  CCcoef = NULL,
  NoTrait = TRUE,
  trace = FALSE,
  TraitWeight = FALSE
)

Arguments

X

A list of omics data each with n subjects.

Trait

An n by 1 trait (phenotype) data for the same samples.

Lambda

Lasso penalty vector with length equals to the number of omics data (X). Lambda needs to be between 0 and 1.

CCcoef

Optional scaling factors for the SmCCA pairwise canonical correlations. If CCcoef = NULL (default), then the objective function is the total sum of all pairwise canonical correlations. It follows the column order of combn(T+1, 2), where T is the total number of omics data.

NoTrait

Whether or not trait (phenotype) information is provided, default is set to TRUE.

trace

Whether to display CCA algorithm trace, default is set to FALSE.

TraitWeight

Whether to return canonical weight for trait (phenotype), default is set to FALSE.

Value

A canonical weight vector with size of p by 1.

Examples

# This function is typically used as an internal function.
# It is also used when performing cross-validation,
# refer to multi-omics vignette for more detail.
# X <- list(X1,X2)
# result <- getCanWeightsMulti(X, Trait = as.matrix(Y), Lambda = c(0.5,0.5), NoTrait = FALSE)
# result <- getCanWeightsMulti(X, Trait = NULL, Lambda = c(0.5,0.5), NoTrait = TRUE)
# cccoef <- c(1,10,10)
# result <- getCanWeightsMulti(X, Trait = as.matrix(Y), CCcoef = cccoef, 
#                              Lambda = c(0.5,0.5), NoTrait = FALSE)