resSep: Select Peptides with the Specified Amino Acid Residue(s) at an Indicated Position

Description

Allows the experimenter to subset peptide data based on a selected amino acid residue or sequence a specified position(s). Requires the experimenter to select the residue(s) and position(s) of interest at a given length or length/charge combination.

Usage

resSep(File,Length,Charge = NULL,Pos,Res)

Arguments

File

An object, generally a data.frame, the vFormat object with peptide and signal data.

Length

An integer, the desired length of the peptides to separate.

Charge

An integer, the desired charge of the peptides to separate. Defaults to Charge = NULL, which carries out length separation only.

Pos

An integer or sequence, the position(s) to check for the residue(s) of interest.

Res

A character input. The residue(s) to check for at the given position(s). The lengths of the arguments Pos and Res must match. Multiple residues are entered as a single character string. Ex: Res = "RA".

Value

A data.frame of the same format as the argument File containing only peptides that contain the specified residue(s) at the indicated position(s).

Details

The lengths of the arguments Pos and Res must match.

Sequence Positions are read from right to left.

Ex: The residue "R" in 5-mer sequence "RSGSG" is at position 5.

When typing in a sequence of interest, it will be in reverse with regard to the displayed sequence.

Ex: Sequence "SR" at positions 4:5 in the 5-mer"RSGSG"

Examples

Run this code

## Example data.frame ##

protEx.resSep <- 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))

## Single Residue Separation ##

resSepEx1 <- resSep(protEx.resSep,12,2,5,"R")

## Positional Sequence Separation ##

resSepEx2 <- resSep(protEx.resSep,12,2,5:6,c("RA"))