cpop_model: CPOP modelling

In kevinwang09/top: Cross Platform Omics Prediction

CPOP modelling

Description

CPOP is consisted of three steps. Step 1 is to select features common to two transformed data. Note the input must be pairwise-differences between the original data columns. Step 2 is to select features in constructed models that shared similar characteristics. Step 3 is to construct a final model used for prediction.

Usage

cpop_model(
  x1,
  x2,
  y1,
  y2,
  w = NULL,
  n_features = 50,
  n_iter = 20,
  alpha = 1,
  family = "binomial",
  s = "lambda.min",
  cpop2_break = TRUE,
  cpop2_type = "sign",
  cpop2_mag = 1,
  cpop1_method = "normal",
  intercept = FALSE,
  z1,
  z2,
  ...
)

Arguments

x1	A data matrix of size n (number of samples) times p (number of features)
x2	A data matrix of size n (number of samples) times p (number of features) Column names should be identical to z1.
y1	A vector of response variable. Same length as the number of rows of x1.
y2	A vector of response variable. Same length as the number of rows of x2.
w	A vector of weights. Default to NULL, which uses 'identity_dist'.
n_features	Breaking the CPOP-Step 1 loop if a certain number of features is reached. Default to 50.
n_iter	Number of iterations in Step 1 and 2. Default to 20.
alpha	The alpha parameter for elastic net models. See the alpha argument in glmnet::glmnet. Default to 1.
family	family of glmnet
s	CV-Lasso lambda choice. Default to "lambda.min", see cv.glmnet in the glmnet package.
cpop2_break	Should CPOP-step2 loop be broken the first time. Default to TRUE.
cpop2_type	Should CPOP-step2 select features based on sign of features of magnitude? Either "sign" (default) or "mag"..
cpop2_mag	a threshold for CPOP-step2 when selecting features based on coefficient difference magnitude. differential betas are removed
cpop1_method	CPOP step 1 selection method. See documentations on 'cpop1'. Default to "Normal".
intercept	Default to FALSE
z1	(Deprecated) a data matrix, columns are pairwise-differences between the original data columns.
z2	(Deprecated) a data matrix, columns are pairwise-differences between the original data columns.
...	Extra parameter settings for cv.glmnet in in the glmnet package.

Value

A CPOP object containing:

• model: the CPOP model as a glmnet object

• coef_tbl: a tibble (data frame) of CPOP feature coefficients

• cpop1_features: a vector of CPOP

Examples

data(cpop_data_binary, package = 'CPOP')
## Loading simulated matrices and vectors
x1 = cpop_data_binary$x1
x2 = cpop_data_binary$x2
y1 = cpop_data_binary$y1
y2 = cpop_data_binary$y2
set.seed(1)
cpop_result = cpop_model(x1 = x1, x2 = x2, y1 = y1, y2 = y2, alpha = 1, n_features = 10)
cpop_result

kevinwang09/top documentation built on April 20, 2022, 3:01 a.m.