so2m_group: Perform Group Sparse O2PLS

In selbouhaddani/OmicsPLS: Data Integration with Two-Way Orthogonal Partial Least Squares

Perform Group Sparse O2PLS

Description

Perform Group Sparse O2PLS

Usage

so2m_group(
  X,
  Y,
  n,
  nx,
  ny,
  groupx = NULL,
  groupy = NULL,
  keepx = NULL,
  keepy = NULL,
  tol = 1e-10,
  max_iterations = 1000,
  max_iterations_sparsity = 1000
)

Arguments

X	Numeric matrix. Vectors will be coerced to matrix with as.matrix (if this is possible)
Y	Numeric matrix. Vectors will be coerced to matrix with as.matrix (if this is possible)
n	Integer. Number of joint PLS components. Must be positive.
nx	Integer. Number of orthogonal components in X. Negative values are interpreted as 0
ny	Integer. Number of orthogonal components in Y. Negative values are interpreted as 0
groupx	Vector. Used when sparse = TRUE. A vector of strings indicating group names of each X-variable. Its length must be equal to the number of variables in X. The order of group names must corresponds to the order of the variables.
groupy	Vector. Used when sparse = TRUE. A vector of strings indicating group names of each Y-variable. The length must be equal to the number of variables in Y. The order of group names must corresponds to the order of the variables.
keepx	Vector. Used when sparse = TRUE. A vector of length n indicating how many variables (or groups if groupx is provided) to keep in each of the joint component of X. If the input is an integer, all the components will have the same amount of variables or groups retained.
keepy	Vector. Used when sparse = TRUE. A vector of length n indicating how many variables (or groups if groupx is provided) to keep in each of the joint component of Y. If the input is an integer, all the components will have the same amount of variables or groups retained.
tol	Double. Threshold for which the NIPALS method is deemed converged. Must be positive.
max_iterations	Integer. Maximum number of iterations for the NIPALS method.
max_iterations_sparsity	Integer. Used when sparse = TRUE. Maximum number of iterations for the NIPALS method for GO2PLS.

Value

A list containing

Tt	Joint X scores
W.	Joint X loadings
U	Joint Y scores
C.	Joint Y loadings
T_Yosc	Orthogonal X scores
P_Yosc.	Orthogonal X loadings
W_Yosc	Orthogonal X weights
U_Xosc	Orthogonal Y scores
P_Xosc.	Orthogonal Y loadings
C_Xosc	Orthogonal Y weights
B_U	Regression coefficient in Tt ~ U
B_T.	Regression coefficient in U ~ Tt
H_TU	Residuals in Tt in Tt ~ U
H_UT	Residuals in U in U ~ Tt
W_gr	Joint weights of X variables at group level. They are the norms of the X-joint loadings per group
C_gr	Joint weights of Y variables at group level. They are the norms of the Y-joint loadings per group

See Also

o2m

selbouhaddani/OmicsPLS documentation built on Aug. 25, 2022, 9:52 p.m.