KSEAapp (version 0.99.0)

KSEA.Barplot: The KSEA App Analysis (KSEA Bar Plot Only)

Description

Takes a formatted phoshoproteomics data input and returns just the summary bar plot of kinase scores

Usage

KSEA.Barplot(KSData, PX, NetworKIN, NetworKIN.cutoff, m.cutoff, p.cutoff,
  export)

Arguments

KSData

the Kinase-Substrate dataset uploaded from the file prefaced with "PSP&NetworKIN_" available from github.com/casecpb/KSEA/

PX

the experimental data file formatted as described in the KSEA.Complete() documentation

NetworKIN

a binary input of TRUE or FALSE, indicating whether or not to include NetworKIN predictions; NetworKIN = TRUE means inclusion of NetworKIN predictions

NetworKIN.cutoff

a numeric value between 1 and infinity setting the minimum NetworKIN score (can be left out if NetworKIN = FALSE)

m.cutoff

a numeric value between 0 and infinity indicating the min. # of substrates a kinase must have to be included in the bar plot output

p.cutoff

a numeric value between 0 and 1 indicating the p-value cutoff for indicating significant kinases in the bar plot

export

a binary input of TRUE or FALSE, indicating whether or not to export the bar plot as a .tiff image into the working directory

Value

creates the bar plot output highlighting key kinase results

References

Casado et al. (2013) Sci Signal. 6(268):rs6

Hornbeck et al. (2015) Nucleic Acids Res. 43:D512-20

Horn et al. (2014) Nature Methods 11(6):603-4

Examples

KSEA.Barplot(KSData, PX, NetworKIN=TRUE, NetworKIN.cutoff=5, 
             m.cutoff=5, p.cutoff=0.01, export=FALSE)
KSEA.Barplot(KSData, PX, NetworKIN=TRUE, NetworKIN.cutoff=5, 
             m.cutoff=8, p.cutoff=0.05, export=TRUE)
KSEA.Barplot(KSData, PX, NetworKIN=FALSE, m.cutoff=2, p.cutoff=0.05, export=TRUE)