VDAP (version 2.0.0)

hitSel: Signal Based Hits Selection for VDAP

Description

Filters the dataset based upon signal from the specified columns. Can be normalized to the average signal of any given peptide at the given concentration. Works for multiple RFU signal inputs or a single Kd input.

Usage

hitSel(File, AvgSet, CutOff, Kd = FALSE)

Arguments

File

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

AvgSet

An integer sequence, defines the columns that contain the concentration data to be used for hits selection. A given peptide will have to qualify as a hit at all given concentration columns to be considered a true peptide hit. Ex: Hits based upon 3 concentrations in columns 5 through 8 = 5:8. If Kd = TRUE, then a single column with the calculated Kd values (generally column 4 created by vFormat) should be entered.

CutOff

A character string that defines the peptide to to normalize to. Hits must be 5 times higher in signal than the given peptide to be returned as hits. Normally "GSG".If Kd = TRUE, hits will be defined as peptides that have a calculated Kd less than one half of the Cutoff peptide

Kd

Toggle that determines if hits will be selected by RFU signal or Kd values. If Kd = TRUE, hits will be defined as peptides that have a calculated Kd less than one half of the Cutoff peptide

Value

A data.frame will be returned only with the peptides that are hits in the given context. (Hits must have Avg signal 5 times greater than the average signal of the peptide specified in the argument Cutoff. Or one fifth (0.2) the Cutoff Kd value if Kd = TRUE)

Examples

protEx.hitSel <- data.frame(Peptides = c("PWRGPWARVGSG","GYNRVGQGSG","PNGYRSGVKGSG","GSG"),
Kd = c(0.2572361,2.8239730,3.3911868,281.3058),C_6uM = c(65011.48,47462.24,24778,2613.03),
C_3uM = c(62637.81,31899.85,21313.67,1161.216),C_1.5uM = c(57893.22,25911.35,10397.99,630.4025))

## Hits selection by RFU signal ##

hitSelRFU <- hitSel(protEx.hitSel,3:5,"GSG",Kd = FALSE)

## Hits selection by calculated Kd ##

hitSelKd <- hitSel(protEx.hitSel,2,"GSG",Kd = TRUE)