vComp: Amino Acid Disbutions by Position at Various Length/Charge
In VDAP: Peptide Array Analysis Tools

Description Usage Arguments Details Value Author(s) See Also Examples

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.

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

vComp.l(Prot, ProtG, Length)

`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

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

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

Cody Moore

vMotif, genPep

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)