Compute aggregated (SmCCA) canonical weights for single omics data with quantitative phenotype (subampling enabled).
Arguments
- X1
An \(n\times p_1\) data matrix (e.g. mRNA) with \(p_1\) features and \(n\) subjects.
- Trait
An \(n\times 1\) trait (phenotype) data matrix for the same \(n\) subjects.
- Lambda1
LASSO penalty parameter for
X1
.Lambda1
needs to be between 0 and 1.- s1
Proportion of features in
X1
to be included, default ats1 = 0.7
.s1
needs to be between 0 and 1, default is set to 0.7.- SubsamplingNum
Number of feature subsamples. Default is 1000. Larger number leads to more accurate results, but at a higher computational cost.
- trace
Whether to display the CCA algorithm trace, default is set to FALSE.
Value
A canonical correlation weight matrix with \(p_1\) rows. Each
column is the canonical correlation weights based on subsampled X1
features. The number of columns is SubsamplingNum
.
Examples
## For illustration, we only subsample 5 times.
set.seed(123)
# Single Omics SmCCA
W1 <- getRobustWeightsSingle(X1, Trait = Y, Lambda1 = 0.05,
s1 = 0.7,
SubsamplingNum = 5, trace = FALSE)