resSep: Select Peptides with the Specified Amino Acid Residue(s) at...
In VDAP: Peptide Array Analysis Tools

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

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.

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

`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"`.

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"

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).

Cody Moore

vSep

## 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"))