Description Usage Arguments Value Author(s) References Examples
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.
1 |
File |
An R object, usually a |
Glob |
A second |
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
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 |
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.
Cody Moore
Plot generation utilizes ggplot2 created by Hadley Wickham [aut, cre] and Winston Chang [aut] and reshape2 created by Hadley Wickham
1 2 3 4 5 6 7 8 9 10 11 | 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)
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