vFormat: Length/Charge/Kd Peptide Calculations and File Assembly

In VDAP: Peptide Array Analysis Tools

Description

Calculates the length, charge, and dissociation rate constant (Kd) for each peptide and assembles the file into a universal format for subsequent VDAP Functions.

Usage

vFormat(x,Kd = FALSE,Concs,Cols)

Arguments

x	An R object, usually a data.frame generally created by the function FLoad()
Kd	Toggle to specify if dissociation rate constants (Kd) values should be calculated. If Kd = FALSE, the nonlinear regression package drc will not be used.
Concs	The concentrations of each column used for Kd calculations, separated by commas. The order must match the relative position of the columns.
Cols	The columns used for Kd calculations, expressed as a sequence. Ex: Columns 2 through 4 = 2:4

Details

The order of concentrations should not matter, as long as they are identical between the Concs and Cols arguments. However, the columns must all be adjacent.

Value

A data.frame will be returned with the Length, charge, and Kd if Kd = TRUE characteristics placed in columns 2 - 4, followed by the signal at each concentration from the x argument. This is followed by quality values such as std.error, p-value, and t-value from the Kd of each peptide. Peptides will remain in column 1.

Note

Uses the R Package: stringr created by Hadley Wickham and drc created by Christian Ritz and Jens C. Strebig

Author(s)

Cody Moore

See Also

Dups, Attrib, KdA.

Examples

## vFormat on example data set ##

protEx <- data.frame(Peptides = c("PWRGPWARVGSG","GYNRVGQGSG","PNGYRSGVKGSG"),
C_6uM = c(65011.48,47462.24,24778), C_3uM = c(62637.81,31899.85,21313.67),
C_1.5uM = c(57893.22,25911.35,10397.99))

## Preformatted protEx ##

      #Peptides    C_6uM    C_3uM  C_1.5uM
#1 PWRGPWARVGSG 65011.48 62637.81 57893.22
#2   GYNRVGQGSG 47462.24 31899.85 25911.35
#3 PNGYRSGVKGSG 24778.00 21313.67 10397.99


formatEx <- vFormat(protEx,Kd = TRUE, c(6,3,1.5), 2:4)

## Formatted output ##

       #Peptide Length Charge        Kd    C_6uM    C_3uM  C_1.5uM    Std..Dev   t.value    p.value
#1 PWRGPWARVGSG     12      2 0.2572361 65011.48 62637.81 57893.22 0.008441968 30.471112 0.02088507
#2   GYNRVGQGSG     10      1 2.8239730 47462.24 31899.85 25911.35 1.619385359  1.743855 0.33146423
#3 PNGYRSGVKGSG     12      2 3.3911868 24778.00 21313.67 10397.99 2.522251940  1.344508 0.40711826

VDAP documentation built on May 2, 2019, 5:13 a.m.