QCKd: Quality Control of Peptides Based on Reproducibility and Kd
In VDAP: Peptide Array Analysis Tools

Description Usage Arguments Details Value Author(s) Examples

Filter out peptides based on reproducibility between replicate concentrations and relative dissociation constants (Kd). Peptides must have a signal ratio between 0.5 and 2.0. A second reference file may be loaded with the same peptides referenced against another sample. Peptides are then compared based upon relative Kd value which must be at least one log10 apart.

1 2	QCKd(File1, File2 = NULL, Kd = FALSE, QC = TRUE, ColSet1 = NULL, ColSet2 = NULL, ColSet3 = NULL)

`File1`	An R object, usually a `data.frame` generally created by the function `FLoad()`
`File2`	An R object, usually a `data.frame` generally created by the function `FLoad()`
`Kd`	A `logical` value, if `Kd = TRUE` then peptides will be filtered by Kd against the argument `File2`
`QC`	A `logical` value, if `QC = TRUE` then peptides will be filtered by ratios of signal between replicates. Ratios must be between 0.5 to 2.0 to remain in the dataset.
`ColSet1`	A sequence value, represents the two columns that are replicates at a single concentration. Peptides must fit QC criteria in all given `ColSets` to remain in the dataset. ColSets may be omitted if less than three concentrations are to be compared. Ex: 2:3
`ColSet2`	A sequence value, represents the two columns that are replicates at a single concentration. Peptides must fit QC criteria in all given `ColSets` to remain in the dataset. ColSets may be omitted if less than three concentrations are to be compared. Ex: 6:7
`ColSet3`	A sequence value, represents the two columns that are replicates at a single concentration. Peptides must fit QC criteria in all given `ColSets` to remain in the dataset. ColSets may be omitted if less than three concentrations are to be compared. Ex: 4:5

Either the QC or Kd filter may be applied by itself of both simultaneously.

A data.frame will be returned with peptides filtered out that do not meet the given criteria for either the QC or Kd filters.

Cody Moore

protEx.QCKd <- 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))

## All peptides filtered out due to same Kd value between files ##

QCKdEx <- QCKd(protEx.QCKd, protEx.QCKd,Kd = TRUE, QC = TRUE, ColSet1 = 5:6)

## QC control only ##

QCKdEx <- QCKd(protEx.QCKd, QC = TRUE, ColSet1 = 5:6)