iBAG_results: iBAG_results

In cvraut/iBAGpkg: integrative Bayesian Analysis of the Genome

iBAG_results

Description

R6 class to store and manage the iBAG results. This does not contain a copy of the iBAG_data object.

constructor

Usage

iBAG_results$new()

Methods

Public methods

• iBAG_results$new()

• iBAG_results$get.X()

• iBAG_results$get.Y()

• iBAG_results$get.SS()

• iBAG_results$get.beta_mean()

• iBAG_results$get.beta_incl_prob()

• iBAG_results$get.n_patients()

• iBAG_results$get.n_genes()

• iBAG_results$get.n_data()

• iBAG_results$clone()

---

Method new()

constructor

Usage

iBAG_results$new(
  X = matrix(0, 1, 1),
  Y = c(0),
  SS = list(c(0), c(0), c(0)),
  beta_mean = c(0),
  beta_incl_prob = c(0),
  DEBUG = FALSE,
  validate = TRUE,
  ...
)

Arguments

X

(NULL): the total X matrix generated by the mech model

Y

(NULL): the vector of outcomes that goes into the clinical model

SS

(list(NULL,NULL)): a list of vectors representing the Sum of Squares Error from the mechanistic model.

beta_mean

(NULL): a vector of posterior means for the coefficients from the clinical model.

beta_incl_prob

(NULL): a vector of posterior inclusion probabilities for the beta coefficients.

DEBUG

(FALSE): initialize object in DEBUG model.

validate

(TRUE): validate the data coming in from the constructor (or any of the setters)

...

: ...

Details

This constructs a class containing all the results from the iBAG object. Some additional details:

• SS:

  • The list size is always >2. The 1st element is the SST, the last element is the SSO, the middle elements correspond to the sum of squares from the datasets.

• validate:

  • minimum data required to validate is X,Y,SS (all produced by mechmodel)

    • if this data is not provided will issue warning & set validate to FALSE

  • n_data is derived from length(SS)-2

  • n_patients is derived as the nrow(X)

  • check that ncol(X)%n_data == 0

    • if not throw error

    • if true: n_genes = ncol(X)%/%n_data

  • check that length(Y) == n_patients

    • if not throw error

  • for each item in SS

    • check that length(item) == n_genes

      • if not throw error

  • if beta_mean & beta_incl_prob are included

    • check that their length == ncol(X)

      • if not throw error

  • This does not check that the data is in a numeric form! (Check that yourself) get.X

---

Method get.X()

returns X matrix

Usage

iBAG_results$get.X()

Returns

matrix that should be n_patients rows and n_genes*n_data columns get.Y

---

Method get.Y()

returns Y vector

Usage

iBAG_results$get.Y()

Returns

vector that is n_patients long get.SS

---

Method get.SS()

returns the Sum of Squares mech model results, either all or some of them

Usage

iBAG_results$get.SS(index = NULL)

Arguments

index

(NULL) can be NULL, integer, or string. If NULL returns list, otherwise returns the vector at index

Returns

a vector or a list of vectors get.beta_mean

---

Method get.beta_mean()

returns the vector of posterior beta means

Usage

iBAG_results$get.beta_mean()

Returns

a vector of posterior beta means get.beta_incl_prob

---

Method get.beta_incl_prob()

returns a vector of posterior beta inclusion probabilities

Usage

iBAG_results$get.beta_incl_prob()

Returns

a vector of posterior beta inclusion probabilities get.n_patients

---

Method get.n_patients()

returns the number of patients

Usage

iBAG_results$get.n_patients()

Returns

integer of number of patients get.genes

---

Method get.n_genes()

returns the number of genes

Usage

iBAG_results$get.n_genes()

Returns

integer of number of genes get.n_data

---

Method get.n_data()

returns the number of upstream datasets

Usage

iBAG_results$get.n_data()

Returns

integer of number of upstream datasets

---

Method clone()

The objects of this class are cloneable with this method.

Usage

iBAG_results$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

cvraut/iBAGpkg documentation built on July 26, 2022, 9:55 p.m.