Package 'DCODE'

List Linear n-Peptide Constraints for Overlapping Protein Regions

Description

Traversal graph algorithm for listing linear n-peptide constraints for overlapping protein regions.

Author(s)

S. Lebre

Maintainer: S. Lebre <[email protected]>

References

Lebre and Gascuel, The combinatorics of overlapping genes (freely available from arXiv at:

http://arxiv.org/abs/1602.04971).

Examples

## Not run: 
# 1) Build peptideList, used by function getConstraint.
mydata <- build_data()
aaList <- mydata$aaList
geneticCode <- mydata$geneticCode
peptideList <- mydata$peptideList

# 2) Ask for the constraint induced on a chosen peptide in a chosen overlapping frame

## amino acid contraints 
getConstraint("C", frame = -2, code=geneticCode, pepList=peptideList) 
getConstraint("D", frame = 1, code=geneticCode, pepList=peptideList)

## 3-peptide contraints
getConstraint("CWC",frame = -2, code=geneticCode, pepList=peptideList)

## 5-peptide contraints
getConstraint("CWCCC",frame = -2, code=geneticCode, pepList=peptideList)
	
## End(Not run)

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Function to build the elements aaList, geneticCode, peptideList, used by function getConstraint.

Description

To be run before the first use of function getConstraint. This function generates the variables aaList, geneticCode and peptideList, a list of all the peptides (up to length 5), used by function getConstraint.

Usage

build_data()

Value

aaList	Vector of all amino acids.
geneticCode	A list describing the standard genetic code.
peptideList	A list of all the peptides (up to length 5).

Author(s)

Sophie Lebre <[email protected]>

References

Lebre and Gascuel, The combinatorics of overlapping genes (freely available from arXiv at:

http://arxiv.org/abs/1602.04971).

See Also

getConstraint

Examples

## Not run: 
# 1) Build peptideList, used by function getConstraint.
mydata <- build_data()
aaList <- mydata$aaList
geneticCode <- mydata$geneticCode
peptideList <- mydata$peptideList

# 2) Ask for the constraint induced on a chosen peptide in a chosen overlapping frame

## amino acid contraints 
getConstraint("C", frame = -2, code=geneticCode, pepList=peptideList) 
getConstraint("D", frame = 1, code=geneticCode, pepList=peptideList)

## 3-peptide contraints
getConstraint("CWC",frame = -2, code=geneticCode, pepList=peptideList)

## 5-peptide contraints
getConstraint("CWCCC",frame = -2, code=geneticCode, pepList=peptideList)
	
## End(Not run)

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Internal DCODE Functions

Description

Internal DCODE functions

Details

These are not to be called by the user (or in some cases are just waiting for proper documentation to be written).

---

Function giving the linear constraint associated with the chosen peptide and overlapping frame.

Description

This function prints the linear constraint to which the chosen peptide in the reference frame pep is subject when condisering gene overlap with frameshift frame.

Usage

getConstraint(pep, frame, code, pepList)

Arguments

pep	A chosen n-peptide in the reference frame (with length n<=5 if pepList is generated by function build_data).
frame	The frameshift chosen in {-2, -1, 0, 1, 2}.
code	The code used to translate codons into amino acids (which can be generated by function build_data).
pepList	A list of all the peptide of length 1, 2, 3, ...required by the graph traversal algorithm (which can be generated by function build_data).

Author(s)

Sophie Lebre <[email protected]>

References

Lebre and Gascuel, The combinatorics of overlapping genes (freely available from arXiv at:

http://arxiv.org/abs/1602.04971).

See Also

build_data

Examples

## Not run: 
# 1) Build peptideList, used by function getConstraint.
mydata <- build_data()
aaList <- mydata$aaList
geneticCode <- mydata$geneticCode
peptideList <- mydata$peptideList

# 2) Ask for the constraint induced on a chosen peptide in a chosen overlapping frame

## amino acid contraints 
getConstraint("C", frame = -2, code=geneticCode, pepList=peptideList) 
getConstraint("D", frame = 1, code=geneticCode, pepList=peptideList)

## 3-peptide contraints
getConstraint("CWC",frame = -2, code=geneticCode, pepList=peptideList)

## 5-peptide contraints
getConstraint("CWCCC",frame = -2, code=geneticCode, pepList=peptideList)
	
## End(Not run)

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