Title: LUCID with Multiple Omics Data
Version: 3.0.3
Description: An implementation of estimating the Latent Unknown Clusters By Integrating Multi-omics Data (LUCID) model (Peng (2019) <doi:10.1093/bioinformatics/btz667>). LUCID conducts integrated clustering using exposures, omics information (and outcome information as an option). This package implements three different integration strategies for multi-omics data analysis within the LUCID framework: LUCID early integration (the original LUCID model), LUCID in parallel (intermediate integration), and LUCID in serial (late integration). Automated model selection for each LUCID model is available to obtain the optimal number of latent clusters, and an integrated imputation approach is implemented to handle sporadic and list-wise missingness in multi-omics data. Lasso-type regularity for exposure and omics features were added. S3 methods for summary and plotting functions were fixed. Fixed minor bugs.
Depends: R (≥ 3.6.0)
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2
LazyData: true
Suggests: testthat (≥ 3.0.0)
Config/testthat/edition: 3
Imports: mclust, nnet, boot, jsonlite, networkD3, progress, stats, utils, glasso, glmnet
NeedsCompilation: no
Packaged: 2024-09-23 19:49:22 UTC; qiranjia19961112
Author: Qiran Jia ORCID iD [aut, cre], Yinqi Zhao ORCID iD [aut], David Conti ORCID iD [ths], Jesse Goodrich ORCID iD [ctb]
Maintainer: Qiran Jia <qiranjia@usc.edu>
Repository: CRAN
Date/Publication: 2024-09-23 20:30:02 UTC

I-step of LUCID

Description

Impute missing data in Z by maximizing the likelihood given fixed parameters of LUCID

Usage

Istep_Z(Z, p, mu, sigma, index, lucid_model)

Arguments

Z

an N by P matrix representing the omics data

p

an N by K matrix representing inclusion probability for each latent cluster

mu

an M by K matrix representing cluster-specific means

sigma

an M by M by K array representing cluster-specific covariance

index

an N by M matrix representing missing values in Z

lucid_model

Specifying LUCID model, "early" for early integration, "parallel" for lucid in parallel, "serial" for lucid in serial

Value

a complete dataset of Z

Inference of LUCID model based on bootstrap resampling

Description

Generate R bootstrap replicates of LUCID parameters and derive confidence interval (CI) base on bootstrap. Bootstrap replicates are generated based on nonparameteric resampling, implemented by ordinary method of boot::boot function. Now only achieved for LUCID early integration.

Usage

boot_lucid(
  G,
  Z,
  Y,
  lucid_model = c("early", "parallel", "serial"),
  CoG = NULL,
  CoY = NULL,
  model,
  conf = 0.95,
  R = 100,
  verbose = FALSE
)

Arguments

G

Exposures, a numeric vector, matrix, or data frame. Categorical variable should be transformed into dummy variables. If a matrix or data frame, rows represent observations and columns correspond to variables.

Z

Omics data for LUCID early integration, a numeric matrix or data frame. Rows correspond to observations and columns correspond to variables.

Y

Outcome, a numeric vector. Categorical variable is not allowed. Binary outcome should be coded as 0 and 1.

lucid_model

Specifying LUCID model, "early" for early integration, "parallel" for lucid in parallel, "serial" for LUCID in serial.Now only work for LUCID early. If "parallel" or "serial", the function will do nothing.

CoG

Optional, covariates to be adjusted for estimating the latent cluster. A numeric vector, matrix or data frame. Categorical variable should be transformed into dummy variables.

CoY

Optional, covariates to be adjusted for estimating the association between latent cluster and the outcome. A numeric vector, matrix or data frame. Categorical variable should be transformed into dummy variables.

model

A LUCID model fitted by estimate_lucid.

conf

A numeric scalar between 0 and 1 to specify confidence level(s) of the required interval(s).

R

An integer to specify number of bootstrap replicates for LUCID model. If feasible, it is recommended to set R >= 1000.

verbose

A flag indicates whether detailed information is printed in console. Default is FALSE.

Value

A list, containing the following components:

beta

effect estimate for each exposure

mu

cluster-specific mean for each omics feature

gamma

effect estiamte for the association btween latent cluster and outcome

bootstrap

The boot object returned by boot:boot

Examples


# use simulated data
G <- sim_data$G
Z <- sim_data$Z
Y_normal <- sim_data$Y_normal

# fit lucid model
fit1 <- estimate_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early", 
family = "normal", K = 2,
seed = 1008)

# conduct bootstrap resampling
boot1 <- boot_lucid(G = G, Z = Z, Y = Y_normal, 
lucid_model = "early",model = fit1, R = 100)

# use 90% CI
boot2 <- boot_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early", 
model = fit1, R = 100, conf = 0.9)

Check missing patterns in one layer of omics data Z

Description

Check missing patterns in one layer of omics data Z

Usage

check_na(Z)

Arguments

Z

A data matrix representing one layer of omics data

Value

  1. index:indeces for missing values in the omics data

  2. indicator_na: missing pattern for each observation

  3. impute_flag: - flag to initialize imputation. Only happens when sporadic missing pattern is observed

Fit LUCID models with one or multiple omics layers

Description

EM algorithm to estimate LUCID with one or multiple omics layers

Usage

estimate_lucid(
  lucid_model = c("early", "parallel", "serial"),
  G,
  Z,
  Y,
  CoG = NULL,
  CoY = NULL,
  K,
  init_omic.data.model = "EEV",
  useY = TRUE,
  tol = 0.001,
  max_itr = 1000,
  max_tot.itr = 10000,
  Rho_G = 0,
  Rho_Z_Mu = 0,
  Rho_Z_Cov = 0,
  family = c("normal", "binary"),
  seed = 123,
  init_impute = c("mix", "lod"),
  init_par = c("mclust", "random"),
  verbose = FALSE
)

Arguments

lucid_model

Specifying LUCID model, "early" for early integration, "parallel" for lucid in parallel, "serial" for lucid in serial

G

an N by P matrix representing exposures

Z

Omics data, if "early", an N by M matrix; If "parallel", a list, each element i is a matrix with N rows and P_i features; If "serial", a list, each element i is a matrix with N rows and p_i features or a list with two or more matrices with N rows and a certain number of features

Y

a length N vector

CoG

an N by V matrix representing covariates to be adjusted for G -> X

CoY

an N by K matrix representing covariates to be adjusted for X -> Y

K

Number of latent clusters. If "early", an integer greater or equal to 2; If "parallel",an integer vector, same length as Z, with each element being an interger greater or equal to 2; If "serial", a list, each element is either an integer like that for "early" or an list of integers like that for "parallel", same length as Z

init_omic.data.model

a vector of strings specifies the geometric model of omics data. If NULL, See more in ?mclust::mclustModelNames

useY

logical, if TRUE, EM algorithm fits a supervised LUCID; otherwise unsupervised LUCID.

tol

stopping criterion for the EM algorithm

max_itr

Maximum iterations of the EM algorithm. If the EM algorithm iterates more than max_itr without converging, the EM algorithm is forced to stop.

max_tot.itr

Max number of total iterations for estimate_lucid function. estimate_lucid may conduct EM algorithm for multiple times if the algorithm fails to converge.

Rho_G

A scalar. This parameter is the LASSO penalty to regularize exposures. If user wants to tune the penalty, use the wrapper function lucid. Now only achieved for LUCID early integration.

Rho_Z_Mu

A scalar. This parameter is the LASSO penalty to regularize cluster-specific means for omics data (Z). If user wants to tune the penalty, use the wrapper function lucid.Now only achieved for LUCID early integration.

Rho_Z_Cov

A scalar. This parameter is the graphical LASSO penalty to estimate sparse cluster-specific variance-covariance matrices for omics data (Z). If user wants to tune the penalty, use the wrapper function lucid. Now only achieved for LUCID early integration.

family

The distribution of the outcome

seed

Random seed to initialize the EM algorithm

init_impute

Method to initialize the imputation of missing values in LUCID. mix will use mclust:imputeData to implement EM Algorithm for Unrestricted General Location Model by the mix package to impute the missing values in omics data; lod will initialize the imputation via replacing missing values by LOD / sqrt(2). LOD is determined by the minimum of each variable in omics data.

init_par

For "early", an interface to initialize EM algorithm, if mclust, initiate the parameters using the mclust package, if random, initiate the parameters by drawing from a uniform distribution; For "parallel", mclust is the default for quick convergence; For "serial", each sub-model follows the above depending on it is a "early" or "parallel"

verbose

A flag indicates whether detailed information for each iteration of EM algorithm is printed in console. Default is FALSE.

Value

A list contains the object below:

  1. res_Beta: estimation for G->X associations

  2. res_Mu: estimation for the mu of the X->Z associations

  3. res_Sigma: estimation for the sigma of the X->Z associations

  4. res_Gamma: estimation for X->Y associations

  5. inclusion.p: inclusion probability of cluster assignment for each observation

  6. K: umber of latent clusters for "early"/list of numbers of latent clusters for "parallel" and "serial"

  7. var.names: names for the G, Z, Y variables

  8. init_omic.data.model: pre-specified geometric model of multi-omics data

  9. likelihood: converged LUCID model log likelihood

  10. family: the distribution of the outcome

  11. select: for LUCID early integration only, indicators of whether each exposure and omics feature is selected

  12. useY: whether this LUCID model is supervised

  13. Z: multi-omics data

  14. init_impute: pre-specified imputation method

  15. init_par: pre-specified parameter initialization method

  16. Rho: for LUCID early integration only, pre-specified regularity tuning parameter

  17. N: number of observations

  18. submodel: for LUCID in serial only, storing all the submodels

Examples

i <- 1008
set.seed(i)
G <- matrix(rnorm(500), nrow = 100)
Z1 <- matrix(rnorm(1000),nrow = 100)
Z2 <- matrix(rnorm(1000), nrow = 100)
Z3 <- matrix(rnorm(1000), nrow = 100)
Z4 <- matrix(rnorm(1000), nrow = 100)
Z5 <- matrix(rnorm(1000), nrow = 100)
Z <- list(Z1 = Z1, Z2 = Z2, Z3 = Z3, Z4 = Z4, Z5 = Z5)
Y <- rnorm(100)
CoY <- matrix(rnorm(200), nrow = 100)
CoG <- matrix(rnorm(200), nrow = 100)
fit1 <- estimate_lucid(G = G, Z = Z, Y = Y, K = list(2,2,2,2,2),
lucid_model = "serial",
family = "normal",
seed = i,
CoG = CoG, CoY = CoY,
useY = TRUE)

Impute missing data by optimizing the likelihood function

Description

Impute missing data by optimizing the likelihood function

Usage

fill_data(obs, mu, sigma, p, index, lucid_model)

Arguments

obs

a vector of length M

mu

a matrix of size M x K

sigma

a matrix of size M x M x K

p

a vector of length K

index

a vector of length M, indicating whether a value is missing or not in the raw data

lucid_model

Specifying LUCID model, "early" for early integration, "parallel" for lucid in parallel, "serial" for lucid in serial

Value

an observation with updated imputed value

generate bootstrp ci (normal, basic and percentile)

Description

generate bootstrp ci (normal, basic and percentile)

Usage

gen_ci(x, conf = 0.95)

Arguments

x

an object return by boot function

conf

A numeric scalar between 0 and 1 to specify confidence level(s) of the required interval(s).

Value

a matrix, the first column is t0 statistic from original model

Fit a lucid model for integrated analysis on exposure, outcome and multi-omics data, allowing for tuning

Description

Fit a lucid model for integrated analysis on exposure, outcome and multi-omics data, allowing for tuning

Usage

lucid(
  G,
  Z,
  Y,
  CoG = NULL,
  CoY = NULL,
  family = c("normal", "binary"),
  K = 2,
  lucid_model = c("early", "parallel", "serial"),
  Rho_G = 0,
  Rho_Z_Mu = 0,
  Rho_Z_Cov = 0,
  verbose_tune = FALSE,
  ...
)

Arguments

G

Exposures, a numeric vector, matrix, or data frame. Categorical variable should be transformed into dummy variables. If a matrix or data frame, rows represent observations and columns correspond to variables.

Z

Omics data. If "early", an N by M matrix; If "parallel", a list, each element i is a matrix with N rows and P_i features; If "serial", a list, each element i is a matrix with N rows and p_i features or a list with two or more matrices with N rows and a certain number of features If "serial", a list, each element is a matrix with N rows or a list with two or more matrices with N rows

Y

Outcome, a numeric vector. Categorical variable is not allowed. Binary outcome should be coded as 0 and 1.

CoG

Optional, covariates to be adjusted for estimating the latent cluster. A numeric vector, matrix or data frame. Categorical variable should be transformed into dummy variables.

CoY

Optional, covariates to be adjusted for estimating the association between latent cluster and the outcome. A numeric vector, matrix or data frame. Categorical variable should be transformed into dummy variables.

family

Distribution of outcome. For continuous outcome, use "normal"; for binary outcome, use "binary". Default is "normal".

K

Number of latent clusters to be tuned. For lucid_model = "early", number of latent clusters (should be greater or equal than 2). Either an integer or a vector of integer. If K is a vector, model selection on K is performed. For lucid_model = "parallel",a list with vectors of integers or just integers, same length as Z, if the element itself is a vector, model selection on K is performed; For lucid_model = "serial", a list, each element is either an integer or an list of integers, same length as Z, if the smallest element (integer) itself is a vector, model selection on K is performed

lucid_model

Specifying LUCID model, "early" for early integration, "parallel" for lucid in parallel, "serial" for lucid in serial

Rho_G

A scalar or a vector. This parameter is the LASSO penalty to regularize exposures. If it is a vector, lucid will call tune_lucid to conduct model selection and variable selection. User can try penalties from 0 to 1. Work for LUCID early only.

Rho_Z_Mu

A scalar or a vector. This parameter is the LASSO penalty to regularize cluster-specific means for omics data (Z). If it is a vector, lucid will call tune_lucid to conduct model selection and variable selection. User can try penalties from 1 to 100. Work for LUCID early only.

Rho_Z_Cov

A scalar or a vector. This parameter is the graphical LASSO penalty to estimate sparse cluster-specific variance-covariance matrices for omics data (Z). If it is a vector, lucid will call tune_lucid to conduct model selection and variable selection. User can try penalties from 0 to 1. Work for LUCID early only.

verbose_tune

A flag to print details of tuning process.

...

Other parameters passed to estimate_lucid

Value

An optimal LUCID model

  1. res_Beta: estimation for G->X associations

  2. res_Mu: estimation for the mu of the X->Z associations

  3. res_Sigma: estimation for the sigma of the X->Z associations

  4. res_Gamma: estimation for X->Y associations

  5. inclusion.p: inclusion probability of cluster assignment for each observation

  6. K: umber of latent clusters for "early"/list of numbers of latent clusters for "parallel" and "serial"

  7. var.names: names for the G, Z, Y variables

  8. init_omic.data.model: pre-specified geometric model of multi-omics data

  9. likelihood: converged LUCID model log likelihood

  10. family: the distribution of the outcome

  11. select: for LUCID early integration only, indicators of whether each exposure and omics feature is selected

  12. useY: whether this LUCID model is supervised

  13. Z: multi-omics data

  14. init_impute: pre-specified imputation method

  15. init_par: pre-specified parameter initialization method

  16. Rho: for LUCID early integration only, pre-specified regularity tuning parameter

  17. N: number of observations

  18. submodel: for LUCID in serial only, storing all the submodels

Examples


# LUCID early integration
G <- sim_data$G
Z <- sim_data$Z
Y_normal <- sim_data$Y_normal
Y_binary <- sim_data$Y_binary
cov <- sim_data$Covariate

# fit lucid model
fit1 <- lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early", family = "normal")
fit2 <- lucid(G = G, Z = Z, Y = Y_binary, lucid_model = "early", family = "binary", useY = FALSE)

# including covariates
fit3 <- lucid(G = G, Z = Z, Y = Y_binary, lucid_model = "early", family = "binary", CoG = cov)
fit4 <- lucid(G = G, Z = Z, Y = Y_binary, lucid_model = "early", family = "binary", CoY = cov)

# tune K
fit5 <- lucid(G = G, Z = Z, Y = Y_binary, lucid_model = "early", family = "binary", K = 2:3)

# variable selection
fit6 <- lucid(G = G, Z = Z, Y = Y_binary, lucid_model = "early", 
family = "binary", Rho_G = seq(0.01, 0.02, by = 0.01))

# LUCID in parallel
i <- 1008
set.seed(i)
G <- matrix(rnorm(500), nrow = 100)
Z1 <- matrix(rnorm(1000),nrow = 100)
Z2 <- matrix(rnorm(1000), nrow = 100)
Z <- list(Z1 = Z1, Z2 = Z2)
CoY <- matrix(rnorm(200), nrow = 100)
CoG <- matrix(rnorm(200), nrow = 100)
Y <- rnorm(100)
best_parallel <- lucid(G = G, Z = Z, Y = Y, K = list(2:3,2),
CoG = CoG, CoY = CoY, lucid_model = "parallel",
family = "normal", init_omic.data.model = "VVV",
seed = i, init_impute = "mix", init_par = "mclust",
useY = TRUE)

# LUCID in serial
best_serial <- lucid(G = G, Z = Z, Y = Y, K = list(2:3,2),
CoG = CoG, CoY = CoY, lucid_model = "serial",
family = "normal", init_omic.data.model = "VVV",
seed = i, init_impute = "mix", init_par = "mclust",
useY = TRUE)

Visualize LUCID model through a Sankey diagram

Description

In the Sankey diagram, each node either represents a variable (exposure, omics or outcome) or a latent cluster. Each line represents an association. The color of the node represents variable type, either exposure, omics or outcome. The width of the line represents the effect size of a certain association; the color of the line represents the direction of a certain association. Only work for LUCID early for now.

Usage

plot(x, ...)

Arguments

x

A LUCID model fitted by estimate_lucid

...

Additional arguments to specify colors and fontsize

Value

A DAG graph created by sankeyNetwork

Examples

# prepare data
G <- sim_data$G
Z <- sim_data$Z
Y_normal <- sim_data$Y_normal
Y_binary <- sim_data$Y_binary
cov <- sim_data$Covariate

# plot lucid model
fit1 <- estimate_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early", 
CoY = NULL, family = "normal", K = 2, seed = 1008)
plot(fit1)

# change node color
plot(fit1, G_color = "yellow")
plot(fit1, Z_color = "red")

# change link color
plot(fit1, pos_link_color = "red", neg_link_color = "green")

Predict cluster assignment and outcome based on LUCID model using new data of G,Z,(Y). If g_computation, predict cluster assignment, omics data, and outcome based on LUCID model using new data of G only This function can also be use to extract X assignment is using training data G,Z,Y as input.

Description

Predict cluster assignment and outcome based on LUCID model using new data of G,Z,(Y). If g_computation, predict cluster assignment, omics data, and outcome based on LUCID model using new data of G only This function can also be use to extract X assignment is using training data G,Z,Y as input.

Usage

predict_lucid(
  model,
  lucid_model = c("early", "parallel", "serial"),
  G,
  Z,
  Y = NULL,
  CoG = NULL,
  CoY = NULL,
  response = TRUE,
  g_computation = FALSE,
  verbose = FALSE
)

Arguments

model

A model fitted and returned by estimate_lucid

lucid_model

Specifying LUCID model, "early" for early integration, "parallel" for lucid in parallel "serial" for lucid in serial.

G

Exposures, a numeric vector, matrix, or data frame. Categorical variable should be transformed into dummy variables. If a matrix or data frame, rows represent observations and columns correspond to variables.

Z

Omics data, if "early", an N by M matrix; If "parallel", a list, each element i is a matrix with N rows and P_i features; If "serial", a list, each element i is a matrix with N rows and p_i features or a list with two or more matrices with N rows and a certain number of features

Y

Outcome, a numeric vector. Categorical variable is not allowed. Binary outcome should be coded as 0 and 1.

CoG

Optional, covariates to be adjusted for estimating the latent cluster. A numeric vector, matrix or data frame. Categorical variable should be transformed into dummy variables.

CoY

Optional, covariates to be adjusted for estimating the association between latent cluster and the outcome. A numeric vector, matrix or data frame. Categorical variable should be transformed into dummy variables.

response

If TRUE, when predicting binary outcome, the response will be returned. If FALSE, the linear predictor is returned.

g_computation

If TRUE, the prediction only uses information on G.

verbose

A flag indicates whether detailed information is printed in console. Default is FALSE.

Value

A list containing the following components:

  1. inclusion.p: A list of inclusion probabilities for each sub-model in the LUCID model.

  2. pred.x: A list of predicted values for the data matrix G.

  3. pred.y: Predicted values for the response variable Y (if response is TRUE).

  4. pred.z: Predicted values for the omics variables Z (if g_computation is TRUE).

Examples

# prepare data
G <- sim_data$G
Z <- sim_data$Z
Y_normal <- sim_data$Y_normal

# fit lucid model
fit1 <- estimate_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early", K = 2, family = "normal")

# prediction on training set
pred1 <- predict_lucid(model = fit1, G = G, Z = Z, Y = Y_normal, lucid_model = "early")
pred2 <- predict_lucid(model = fit1, G = G, Z = Z, lucid_model = "early")

Print the output of LUCID in a nicer table

Description

Print the output of LUCID in a nicer table

Usage

## S3 method for class 'sumlucid_early'
print(x, ...)

Arguments

x

An object returned by summary

...

Other parameters to be passed to print.sumlucid_serial

Value

A nice table/several nice tables of the summary of the LUCID model

Examples


# use simulated data
G <- sim_data$G
Z <- sim_data$Z
Y_normal <- sim_data$Y_normal

# fit lucid model
fit1 <- estimate_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early", family = "normal", K = 2,
seed = 1008)

# conduct bootstrap resampling
boot1 <- boot_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early", model = fit1, R = 100)

# print the summary of the lucid model in a table
temp <- summary(fit1)
print(temp)

Print the output of LUCID in a nicer table

Description

Print the output of LUCID in a nicer table

Usage

## S3 method for class 'sumlucid_parallel'
print(x, ...)

Arguments

x

An object returned by summary

...

Other parameters to be passed to print.sumlucid_parallel

Value

A nice table/several nice tables of the summary of the LUCID model

Print the output of LUCID in a nicer table

Description

Print the output of LUCID in a nicer table

Usage

## S3 method for class 'sumlucid_serial'
print(x, ...)

Arguments

x

An object returned by summary

...

Other parameters to be passed to print.sumlucid_serial

Value

A nice table/several nice tables of the summary of the LUCID model

A simulated dataset for LUCID

Description

This is an example dataset to illustrate LUCID model. It is simulated by assuming there are 2 latent clusters in the data. We assume the exposures are associated with latent cluster which ultimately affects the PFAS concentration and liver injury in children. The latent clusters are also characterized by differential levels of metabolites.

Usage

sim_data

Format

A list with 5 matrices corresponding to exposures (G), omics data (Z), a continuous outcome, a binary outcome and 2 covariates (can be used either as CoX or CoY). Each matrice contains 2000 observations.

G

10 exposures

Z

10 metabolites

Y_normal

Outcome, PFAS concentration in children

Y_bninary

Bianry outcome, liver injury status

Covariates

2 continous covariates, can be treated as either CoX or CoY

X

Latent clusters

A simulated HELIX dataset for LUCID

Description

The Human Early-Life Exposome (HELIX) project is multi-center research project that aims to characterize early-life environmental exposures and associate these with omics biomarkers and child health outcomes (Vrijheid, 2014. doi: 10.1289/ehp.1307204). We used a subset of HELIX data from Exposome Data Challenge 2021 (hold by ISGlobal) as an example to illustrate LUCID model.

Usage

simulated_HELIX_data

Format

A list with 4 matrices corresponding to exposures (G), omics data (Z), outcome (Y) and covariates (CoY), a total of 420 observations

exposure

1 exposures measuring the maternal exposure to utero mercury.

omics

10 methylomics, 10 transcriptomics, 10 miRNA

outcome

A continuous outcome as an indicator of metabolic-dysfunciton-associated fatty liver disease (MAFLD)

covariate

3 covariates including fish_preg_ter, child sex, maternal age

Summarize results of the early LUCID model

Description

Summarize results of the early LUCID model

Usage

## S3 method for class 'early_lucid'
summary(object, ...)

Arguments

object

A LUCID model fitted by estimate_lucid

...

Additional argument of boot.se, which is an object returned by boot_lucid

Value

A list, containing the extracted key parameters from the LUCID model that can be used to print the summary table

Examples


# use simulated data
G <- sim_data$G
Z <- sim_data$Z
Y_normal <- sim_data$Y_normal

# fit lucid model
fit1 <- estimate_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early", family = "normal", K = 2,
seed = 1008)

# conduct bootstrap resampling
boot1 <- boot_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early", model = fit1, R = 100)

# summarize lucid model
summary(fit1)

# summarize lucid model with bootstrap CIs
summary(fit1, boot.se = boot1)

Summarize results of the parallel LUCID model

Description

Summarize results of the parallel LUCID model

Usage

## S3 method for class 'lucid_parallel'
summary(object, ...)

Arguments

object

A LUCID model fitted by estimate_lucid

...

Additional argument of boot.se, which is an object returned by boot_lucid

Value

A list, containing the extracted key parameters from the LUCID model that can be used to print the summary table

Summarize results of the serial LUCID model

Description

Summarize results of the serial LUCID model

Usage

## S3 method for class 'lucid_serial'
summary(object, ...)

Arguments

object

A LUCID model fitted by estimate_lucid

...

Additional argument of boot.se, which is an object returned by boot_lucid

Value

A list, containing the extracted key parameters from the LUCID model that can be used to print the summary table

A wrapper function to perform model selection for LUCID

Description

Given a grid of K and L1 penalties (incluing Rho_G, Rho_Z_mu and Rho_Z_Cov; for LUCID early only), fit LUCID model over all combinations of K and L1 penalties to determine the optimal penalty. Note that the input of the grid of K differs for different LUCID models. i.e. For LUCID Early, K = 3:5; for LUCID in parallel, K = list(2:3, 2:3); for LUCID in serial, K = list(list(2:3,2),2:3)

Usage

tune_lucid(
  G,
  Z,
  Y,
  CoG = NULL,
  CoY = NULL,
  family = c("normal", "binary"),
  K,
  lucid_model = c("early", "parallel", "serial"),
  Rho_G = 0,
  Rho_Z_Mu = 0,
  Rho_Z_Cov = 0,
  verbose_tune = FALSE,
  ...
)

Arguments

G

Exposures, a numeric vector, matrix, or data frame. Categorical variable should be transformed into dummy variables. If a matrix or data frame, rows represent observations and columns correspond to variables.

Z

Omics data, if "early", an N by M matrix; If "parallel", a list, each element i is a matrix with N rows and P_i features; If "serial", a list, each element i is a matrix with N rows and p_i features or a list with two or more matrices with N rows and a certain number of features

Y

Outcome, a numeric vector. Categorical variable is not allowed. Binary outcome should be coded as 0 and 1.

CoG

Optional, covariates to be adjusted for estimating the latent cluster. A numeric vector, matrix or data frame. Categorical variable should be transformed into dummy variables.

CoY

Optional, covariates to be adjusted for estimating the association between latent cluster and the outcome. A numeric vector, matrix or data frame. Categorical variable should be transformed into dummy variables.

family

Distribution of outcome. For continuous outcome, use "normal"; for binary outcome, use "binary". Default is "normal".

K

Number of latent clusters. If "early", an integer;If "parallel",a list, each element is an integer/integer vector, same length as Z; If "serial", a list, each element is either an integer or an list of integers, same length as Z. If K is given as a grid, the input of the grid of K differs for different LUCID models. i.e. For LUCID Early, K = 3:5; for LUCID in parallel, K = list(2:3, 2:3); for LUCID in serial, K = list(list(2:3,2),2:3)

lucid_model

Specifying LUCID model, "early" for early integration, "parallel" for lucid in parallel, "serial" for lucid in serial

Rho_G

A scalar or a vector. This parameter is the LASSO penalty to regularize exposures. If it is a vector, tune_lucid will conduct model selection and variable selection. User can try penalties from 0 to 1. Work for LUCID early only.

Rho_Z_Mu

A scalar or a vector. This parameter is the LASSO penalty to regularize cluster-specific means for omics data (Z). If it is a vector, tune_lucid will conduct model selection and variable selection. User can try penalties from 1 to 100. Work for LUCID early only.

Rho_Z_Cov

A scalar or a vector. This parameter is the graphical LASSO penalty to estimate sparse cluster-specific variance-covariance matrices for omics data (Z). If it is a vector, tune_lucid will conduct model selection and variable selection. User can try penalties from 0 to 1. Work for LUCID early only.

verbose_tune

A flag to print details of tuning process.

...

Other parameters passed to estimate_lucid

Value

A list:

best_model

the best model over different combination of tuning parameters

tune_list

a data frame contains combination of tuning parameters and c orresponding BIC

res_model

a list of LUCID models corresponding to each combination of tuning parameters

Examples

## Not run: 
# use simulated data
G <- sim_data$G
Z <- sim_data$Z
Y_normal <- sim_data$Y_normal

# find the optimal model over the grid of K
tune_K <- tune_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early",
 useY = FALSE, tol = 1e-2,
seed = 1, K = 2:3)

# tune penalties
tune_Rho_G <- tune_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early",
 useY = FALSE, tol = 1e-2,
seed = 1, K = 2, Rho_G = c(0.1, 0.2))
tune_Rho_Z_Mu <- tune_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early", 
useY = FALSE, tol = 1e-2,
seed = 1, K = 2, Rho_Z_Mu = c(10, 20))
tune_Rho_Z_Cov <- tune_lucid(G = G, Z = Z, Y = Y_normal, lucid_model = "early", 
useY = FALSE, tol = 1e-2,
seed = 1, K = 2, Rho_Z_Cov = c(0.1, 0.2))

## End(Not run)