getConstraint: Function giving the linear constraint associated with the...

Description Usage Arguments Author(s) References See Also Examples

View source: R/getConstraint.R

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

1

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 <sophie.lebre@umontpellier.fr>

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

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	## 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)

DCODE documentation built on May 29, 2017, 9:32 a.m.