VDAP (version 2.0.0)

genPep: Peptide generator based on the output of functions vComp or vMotif

Description

Generates the specified number of peptides whose positional composition is determined by a weighted matrix given by the VDAP functions vComp or vMotif

Usage

genPep(Struct,draw)

Arguments

Struct

The output positional weight matrix from the VDAP functions vComp or vMotif

draw

An integer value, the number of peptides to be generated

Value

A data.frame containing the number of peptides given by the argument draw in a single column.

Details

The final composition of residues at each position should reflect the relative weight present in the argument Struct, as the relative weights at each position are used to weight the sampling of amino acids at each position.

See Also

vComp,vMotif

Examples

protEx.Motif <- data.frame(Peptides = c("PWRGPWARVGSG","GYNRVGQGSG","PNGYRSGVKGSG","GSG"),
Length = c(12,10,12,3),Charge = c(2,1,2,0),Kd = c(0.2572361,2.8239730,3.3911868,281.3058),
C_6uM = c(65011.48,47462.24,24778,2613.03),C_6uM2 = c(62637.81,20723.85,21313.67,2300.216))

## Output weighted matrix generated by vMotif ##

vMotif.lcEx <- vMotif.lc(protEx.Motif,protEx.Motif, 12,2,5,Kd = FALSE)

## Generation of 10 peptides based on vMotif matrix weights##

genPepEx <- genPep(vMotif.lcEx,10)