build_data: Function to build the elements 'aaList', 'geneticCode',...

Description Usage Value Author(s) References See Also Examples

View source: R/build_data.R

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

1

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 <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

getConstraint

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.