VDAP (version 2.0.0)

vMotif: Generate Signal Weighted Amino Acid Heat Maps by Position

Description

Generate signal weighted amino acid composition maps by postion at specific length or length/charge combinations. Weights are compared to the global distribution of peptides at the particular length or length/charge.

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 and/or signal while weights below 1 indicate lower probability at the given position and/or signal.

When Kd = TRUE, weighting by Kd instead of signal is performed. Weights are generated using (1/Kd) since lower Kd values generally indicate higher affinity interactions, and would correlate with higher signal.

Usage

vMotif.lc(Prot, ProtG, Length, Charge, SigCol, Kd = FALSE)
vMotif.l(Prot, ProtG, Length, SigCol, Kd = FALSE)

Arguments

Prot

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

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.

Charge

An integer value, indicating the desired charge to analyze

Length

An integer value, indicating the desired peptide length to analyze

SigCol

An Integer value, indicating the column that contains the desired signal data at a given concentration

Kd

An logical value, indicating if weights should be generated using signal or Kd data. Effects signal weighting behavior. If Kd = TRUE, weights are generated using 1/SigCol.

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

See Also

vComp

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))

## vMotif Length/Charge and Length Signal Examples ##

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

vMotif.lEx <- vMotif.l(protEx.Motif,protEx.Motif, Length = 12,SigCol = 5,Kd = FALSE)

## vMotif Length/Charge Kd Example ##

vMotif.lcEx <- vMotif.lc(protEx.Motif,protEx.Motif, Length = 12,Charge = 2, SigCol = 5,Kd = TRUE)