vComp {VDAP}

Amino Acid Disbutions by Position at Various Length/Charge

Description

Generates the probability of each amino acid to appear in each position within a peptide of a specific length or length/charge combination. Can either be the raw probability or the ratio between the probabilities of 2 peptide sets.

Weights are centered at 1, meaning that there is no change in probability or signal from the global set. Weights above 1 indicate higher probability at the given position while weights below 1 indicate lower probability at the given position.

Usage

vComp.lc(Prot, ProtG, Length, Charge)

vComp.l(Prot, ProtG, Length)

Arguments

Prot

An R object, generally a data.frame. Contains peptides that are considered "hits" or selected peptides with their length,charge, and signal information.

ProtG

An R object, generally a data.frame. Contains the set of peptides from which the argument Prot were selected with their corresponding length, charge, and signal information.

Length

An integer value, indicating the desired peptide length to analyze

Charge

An integer value, indicating the desired charge to analyze

Details

If raw probabilities are desired, the same object can be loaded into both the Prot and ProtG arguments.

Value

Returns a data.frame that shows weights for each amino acid at each position within the peptide of the selected length. Also output a positional heatmap using the package ggplot2

Author(s)

Cody Moore

See Also

vMotif, genPep

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))

## Length/Charge Example ##

vComp.lcEx <- vComp.lc(protEx.Motif,protEx.Motif, 12,2)

## Length Example ##

vComp.lEx <- vComp.l(protEx.Motif,protEx.Motif, 12)