singleStructureGenerator {MethEvolSIM}R Documentation

singleStructureGenerator

Description

an R6 class representing a single genomic structure

Methods

Public methods

Method init_neighbSt()

Public method: Initialization of $neighbSt

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

Returns

A new singleStructureGenerator object.

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(
  leftNeighbSt,
  rightNeighbSt
)
Arguments
leftNeighbSt

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

rightNeighbSt

$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(
  leftNeighbSt,
  rightNeighbSt
)
Arguments
leftNeighbSt

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

rightNeighbSt

$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 number of events sampled and a dataframe with the position(s) affected, new state and old methylation state.

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 flags(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 clone()

The objects of this class are cloneable with this method.

Usage
singleStructureGenerator$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

[Package MethEvolSIM version 0.1.4 Index]