lcScan {VDAP}

Signal or Kd Distributions separated by Length/Charge attributes

Description

Calculates the mean with standard error, and population peptides at each length/charge combination within a VDAP dataset. If the argument Glob = TRUE, average signals will be compared against a global set of peptides and p - values will be calculated for hypoethesis testing. lcScan will also return a plot for visualization of signal, population, and hypothesis testing.

Usage

lcScan(File,Glob = NULL, Conc = 5, Kd = FALSE)

Arguments

File

An R object, usually a data.frame generally created by the function FLoad()

Glob

A second data.frame with the global set of peptides. If the original File argument contains peptides hits, Glob should contain the dataset before hits were filtered out.

Conc

The column contianing the concentration or Kd data to be analyzed, an integer. Default is column 5 which is generally the highest concentration average according to the default formatting function vFormat

Ex: Column 1 = 1

Kd

Toggle to calculate by a defined signal column or by calculated Kd values, effects final plot behavior and labels. If Kd = TRUE, then the arguement Conc should be set to 4 if the file was formatted by the default formatting function vFormat.

Value

A data.frame will be returned with columns for the mean, standard error, and population of peptides at each length/charge combination that can be exported for further analysis. Also uitilizes ggplot2 and reshape2 to create a heat map plot that shows the signal distribution with corresponding populations that can be exported.

Author(s)

Cody Moore

References

Plot generation utilizes ggplot2 created by Hadley Wickham [aut, cre] and Winston Chang [aut] and reshape2 created by Hadley Wickham

Examples

protEx.lcScan <- 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))

## Signal length/charge Analysis ##

lcScanEx <- lcScan(protEx.lcScan)

## Kd length/charge Analysis ##

lcScanEx <- lcScan(protEx.lcScan, Conc = 4, Kd = TRUE)