DCODE (version 1.0)

getConstraint: 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).

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)