singleStructureGenerator: singleStructureGenerator

In MethEvolSIM: Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies

singleStructureGenerator

Description

an R6 class representing a single genomic structure

Public fields

testing_output

Public attribute: Testing output for initialize

Methods

Public methods

• singleStructureGenerator$init_neighbSt()

• singleStructureGenerator$initialize_ratetree()

• singleStructureGenerator$new()

• singleStructureGenerator$set_myCombiStructure()

• singleStructureGenerator$get_seq()

• singleStructureGenerator$get_seqFirstPos()

• singleStructureGenerator$get_seq2ndPos()

• singleStructureGenerator$get_seqLastPos()

• singleStructureGenerator$get_seq2ndButLastPos()

• singleStructureGenerator$get_combiStructure_index()

• singleStructureGenerator$update_interStr_firstNeighbSt()

• singleStructureGenerator$update_interStr_lastNeighbSt()

• singleStructureGenerator$get_eqFreqs()

• singleStructureGenerator$SSE_evol()

• singleStructureGenerator$get_transMat()

• singleStructureGenerator$IWE_evol()

• singleStructureGenerator$get_alpha_pI()

• singleStructureGenerator$get_beta_pI()

• singleStructureGenerator$get_alpha_mI()

• singleStructureGenerator$get_beta_mI()

• singleStructureGenerator$get_alpha_pNI()

• singleStructureGenerator$get_beta_pNI()

• singleStructureGenerator$get_alpha_mNI()

• singleStructureGenerator$get_beta_mNI()

• singleStructureGenerator$get_alpha_Ri()

• singleStructureGenerator$get_iota()

• singleStructureGenerator$get_Ri_values()

• singleStructureGenerator$get_Q()

• singleStructureGenerator$get_siteR()

• singleStructureGenerator$get_neighbSt()

• singleStructureGenerator$update_ratetree_otherStr()

• singleStructureGenerator$get_Qi()

• singleStructureGenerator$get_seqSt_leftneighb()

• singleStructureGenerator$get_seqSt_rightneighb()

• singleStructureGenerator$cftp_all_equal()

• singleStructureGenerator$set_seqSt_update_neighbSt()

• singleStructureGenerator$reset_seq()

• singleStructureGenerator$clone()

---

Method init_neighbSt()

Public method: Initialization of $neighbSt

This fuction initiates each CpG position $neighbSt as encoded in $mapNeighbSt_matrix

It uses $update_neighbSt which updates for each sequence index, the neighbSt of left and right neighbors This means that it updates position 2, then 1 and 3, then 2 and 4.. Therefore, if the combiStructure instance has several singleStr instances within and the first has length 1, the $neighbSt of that position of the first singleStr instance is initialized when the method is called from the second singleStr instance

Positions at the edge of the entire simulated sequence use their only neighbor as both neighbors.

Usage

singleStructureGenerator$init_neighbSt()

Returns

NULL

---

Method initialize_ratetree()

Public method: Initialization of $ratetree

This function initializes $ratetree

Usage

singleStructureGenerator$initialize_ratetree()

Returns

NULL

---

Method new()

Create a new singleStructureGenerator object.

Note that this object is typically generated withing a combiStructureGenerator object.

Usage

singleStructureGenerator$new(
  globalState,
  n,
  eqFreqs = NULL,
  combiStr = NULL,
  combiStr_index = NULL,
  params = NULL,
  testing = FALSE
)

Arguments

globalState

Character. Structure's favored global state: "M" for methylated (island structures) / "U" for unmethylated (non-island structures).

n

Numerical Value. Number of CpG positions

eqFreqs

Default NULL. When given: numerical vector with structure's methylation state equilibrium frequencies (for unmethylated, partially methylated and methylated)

combiStr

Default NULL. When initiated from combiStructureGenerator: object of class combiStructureGenerator containing it

combiStr_index

Default NULL. When initiated from combiStructureGenerator: index in Object of class combiStructureGenerator

params

Default NULL. When given: data frame containing model parameters

testing

Default FALSE. TRUE for writing in public field of new instance $testing_output

Returns

A new singleStructureGenerator object.

---

Method set_myCombiStructure()

Public method: Set my_combiStructure. Assigns given combi instance to private field my_combiStructure

Usage

singleStructureGenerator$set_myCombiStructure(combi)

Arguments

combi

instance of combiStructureGenerator

Returns

NULL

---

Method get_seq()

Public method: Get object's methylation state sequence

Encoded with 1 for unmethylated, 2 for partially methylated and 3 for methylated

Usage

singleStructureGenerator$get_seq()

Returns

vector with equilibrium frequencies of unmethylated, partially methylated and methylated

---

Method get_seqFirstPos()

Public method: Get first sequence position methylation state

Usage

singleStructureGenerator$get_seqFirstPos()

Returns

numerical encoding of first position's methylation state

---

Method get_seq2ndPos()

Public method: Get second sequence position methylation state

Usage

singleStructureGenerator$get_seq2ndPos()

Returns

numerical encoding of second position's methylation state. NULL if position does not exist

---

Method get_seqLastPos()

Public method: Get first sequence position methylation state

Usage

singleStructureGenerator$get_seqLastPos()

Returns

numerical encoding of first position's methylation state

---

Method get_seq2ndButLastPos()

Public method: Get second but last sequence position methylation state

Usage

singleStructureGenerator$get_seq2ndButLastPos()

Returns

numerical encoding of second but last position's methylation state. NULL if position does not exist

---

Method get_combiStructure_index()

Public method: Get index in object of class combiStructureGenerator

Usage

singleStructureGenerator$get_combiStructure_index()

Returns

index in object of class combiStructureGenerator

---

Method update_interStr_firstNeighbSt()

Public method: Update neighbSt of next singleStructureGenerator object within combiStructureGenerator object

This function is used when the last $seq position of a singleStructureGenerator object changes methylation state to update the neighbSt position

Usage

singleStructureGenerator$update_interStr_firstNeighbSt(
  leftNeighb_seqSt,
  rightNeighb_seqSt
)

Arguments

leftNeighb_seqSt

$seq state of left neighbor (left neighbor is in previous singleStructureGenerator object)

rightNeighb_seqSt

$seq state of right neighbor

Returns

NULL

---

Method update_interStr_lastNeighbSt()

Public method: Update neighbSt of previous singleStructureGenerator object within combiStructureGenerator object

Usage

singleStructureGenerator$update_interStr_lastNeighbSt(
  leftNeighb_seqSt,
  rightNeighb_seqSt
)

Arguments

leftNeighb_seqSt

$seq state of right neighbor (left neighbor is in next singleStructureGenerator object)

rightNeighb_seqSt

$seq state of right neighbor

Returns

NULL

---

Method get_eqFreqs()

Public method: Get object's equilibrium Frequencies

Usage

singleStructureGenerator$get_eqFreqs()

Returns

vector with equilibrium frequencies of unmethylated, partially methylated and methylated

---

Method SSE_evol()

Public method. Simulate how CpG dinucleotide methylation state changes due to the SSE process along a time step of length dt

Usage

singleStructureGenerator$SSE_evol(dt, testing = FALSE)

Arguments

dt

time step length.

testing

logical value for testing purposes. Default FALSE.

Returns

default NULL. If testing TRUE it returns a list with the debugNov3.outnumber of events sampled and a dataframe with the position(s) affected, new state and old methylation state.

---

Method get_transMat()

Public Method. Get a transition matrix

Usage

singleStructureGenerator$get_transMat(
  old_eqFreqs,
  new_eqFreqs,
  info,
  testing = FALSE
)

Arguments

old_eqFreqs

numeric vector with 3 frequency values (for old u, p and m)

new_eqFreqs

numeric vector with 3 frequency values (for new u, p and m)

info

character string to indicate where the method is being called

testing

logical value for testing purposes. Default FALSE.

Details

Given a tripple of old equilibrium frequencies and new equilibrium frequencies, generates the corresponding transition matrix.

Returns

transMat. The transition matrix. If testing = TRUE it returns a list. If there was a change in the equilibrium frequencies the list contains the following 7 elements, if not it contains the first 3 elements:

transMat

transition matrix

case

The applied case.

---

Method IWE_evol()

Public Method. Simulate IWE Events

Simulates how CpG Islands' methylation state frequencies change and simultaneous sites change methylation state along a branch of length t according to the SSE-IWE model.

Usage

singleStructureGenerator$IWE_evol(testing = FALSE)

Arguments

testing

logical value for testing purposes. Default FALSE.

Details

The function checks if the methylation equilibrium frequencies (eqFreqs) and sequence observed frequencies (obsFreqs) change after the IWE event. If there is a change in either frequencies, the corresponding change flag eqFreqsChange in the infoIWE list will be set to TRUE.

Returns

If testing = TRUE it returns a list. If there was a change in the equilibrium frequencies the list contains the following 7 elements, if not it contains the first 3 elements:

eqFreqsChange

logical indicating if there was a change in the equilibrium frequencies.

old_eqFreqs

Original equilibrium frequencies before the IWE event.

new_eqFreqs

New equilibrium frequencies after the IWE event.

old_obsFreqs

Original observed frequencies before the IWE event.

new_obsFreqs

New observed frequencies after the IWE event.

IWE_case

Description of the IWE event case.

Mk

Transition matrix used for the IWE event.

---

Method get_alpha_pI()

Public Method.

Usage

singleStructureGenerator$get_alpha_pI()

Returns

Model parameter alpha_pI for sampling island equilibrium frequencies

---

Method get_beta_pI()

Public Method.

Usage

singleStructureGenerator$get_beta_pI()

Returns

Model parameter for sampling island equilibrium frequencies

---

Method get_alpha_mI()

Public Method.

Usage

singleStructureGenerator$get_alpha_mI()

Returns

Model parameter for sampling island equilibrium frequencies

---

Method get_beta_mI()

Public Method.

Usage

singleStructureGenerator$get_beta_mI()

Returns

Model parameter for sampling island equilibrium frequencies

---

Method get_alpha_pNI()

Public Method.

Usage

singleStructureGenerator$get_alpha_pNI()

Returns

Model parameter for sampling non-island equilibrium frequencies

---

Method get_beta_pNI()

Public Method.

Usage

singleStructureGenerator$get_beta_pNI()

Returns

Model parameter for sampling non-island equilibrium frequencies

---

Method get_alpha_mNI()

Public Method.

Usage

singleStructureGenerator$get_alpha_mNI()

Returns

Model parameter for sampling non-island equilibrium frequencies

---

Method get_beta_mNI()

Public Method.

Usage

singleStructureGenerator$get_beta_mNI()

Returns

Model parameter for sampling non-island equilibrium frequencies

---

Method get_alpha_Ri()

Public Method.

Usage

singleStructureGenerator$get_alpha_Ri()

Returns

Model parameter for gamma distribution shape to initialize the 3 $Ri_values

---

Method get_iota()

Public Method.

Usage

singleStructureGenerator$get_iota()

Returns

Model parameter for gamma distribution expected value to initialize the 3 $Ri_values

---

Method get_Ri_values()

Public Method.

Usage

singleStructureGenerator$get_Ri_values()

Returns

The 3 $Ri_values

---

Method get_Q()

Public Method.

Usage

singleStructureGenerator$get_Q(
  siteR = NULL,
  neighbSt = NULL,
  oldSt = NULL,
  newSt = NULL
)

Arguments

siteR

default NULL. Numerical value encoding for the sites rate of independent SSE (1, 2 or 3)

neighbSt

default NULL. Numerical value encoding for the sites neighbouring state (as in mapNeighbSt_matrix)

oldSt

default NULL. Numerical value encoding for the sites old methylation state (1, 2 or 3)

newSt

default NULL. Numerical value encoding for the sites new methylation state (1, 2 or 3)

Returns

With NULL arguments, the list of rate matrices. With non NULL arguments, the corresponding rate of change.

---

Method get_siteR()

Public Method.

Usage

singleStructureGenerator$get_siteR(index = NULL)

Arguments

index

default NULL. Numerical value for the index of the CpG position within the singleStr instance

Returns

with NULL arguments, siteR vector. non NULL arguments, the corresponding siteR

---

Method get_neighbSt()

Public Method.

Usage

singleStructureGenerator$get_neighbSt(index = NULL)

Arguments

index

default NULL. Numerical value for the index of the CpG position within the singleStr instance

Returns

with NULL arguments, neighbSt vector. non NULL arguments, the corresponding neighbSt

---

Method update_ratetree_otherStr()

Public Method. Update ratetree from another singleStructure instance

Usage

singleStructureGenerator$update_ratetree_otherStr(position, rate)

Arguments

position

Numerical value for the index of the CpG position within the singleStr instance

rate

Rate of change to asign to that position

Returns

NULL

---

Method get_Qi()

Public Method. Get list of matrices for SSE process

Usage

singleStructureGenerator$get_Qi(siteR = NULL, oldSt = NULL, newSt = NULL)

Arguments

siteR

default NULL. Numerical value encoding for the sites rate of independent SSE (1, 2 or 3)

oldSt

default NULL. Numerical value encoding for the sites old methylation state (1, 2 or 3)

newSt

default NULL. Numerical value encoding for the sites new methylation state (1, 2 or 3)

Returns

With NULL arguments, the list of SSEi rate matrices. With non NULL arguments, the corresponding rate of change.

---

Method get_seqSt_leftneighb()

Public Method. Decode methylation state of left neighbor form owns neighbSt

Usage

singleStructureGenerator$get_seqSt_leftneighb(index)

Arguments

index

Integer index value for the CpG position within the singleStr instance

Returns

decoded methylation state ($seq) of left neighbor (1, 2 or 3 for unmethylated, partially methylated or methylated)

---

Method get_seqSt_rightneighb()

Public Method. Decode methylation state of left neighbor form owns neighbSt

Usage

singleStructureGenerator$get_seqSt_rightneighb(index)

Arguments

index

Integer index value for the CpG position within the singleStr instance

Returns

decoded methylation state ($seq) of right neighbor (1, 2 or 3 for unmethylated, partially methylated or methylated)

---

Method cftp_all_equal()

Public Method. Make a singleStructure with the same segment lengths and parameters as the focal one but where all states are m or u

Usage

singleStructureGenerator$cftp_all_equal(state, testing = FALSE)

Arguments

state

Character value "U" or "M"

testing

default FALSE. TRUE for testing output

Returns

right neighbSt

---

Method set_seqSt_update_neighbSt()

Public Method. Set the methylation state of a sequence position and update the neighbor's neighbSt. It does NOT update RATETREE

Usage

singleStructureGenerator$set_seqSt_update_neighbSt(
  index,
  newSt,
  testing = FALSE
)

Arguments

index

Numerical value for the index of the CpG position within the singleStr instance

newSt

Numerical value encoding for the sites new methylation state (1, 2 or 3)

testing

default FALSE. TRUE for testing output

Returns

NULL when testing FALSE. Testing output when testing TRUE.

---

Method reset_seq()

Public Method. Resets the sequence states by resampling according to the instance's equilibrium frequencies.

Usage

singleStructureGenerator$reset_seq()

Returns

NULL. The sequence is updated in place.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

singleStructureGenerator$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

MethEvolSIM documentation built on April 12, 2025, 1:30 a.m.