genPep {VDAP}

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

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.

Value

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

Note

The weighted values are squared before being used to weight random residue draws at each position. This is donein order to further penalize peptides that appear less frequently than the global distribution (Have weights < 1), and enrich peptides that appear more often than the global distribution (Have weights > 1).

Author(s)

Cody Moore

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)