KSEA.Complete {KSEAapp} | R Documentation |
The Complete KSEA App Analysis
Description
Takes a formatted phoshoproteomics data input and performs KSEA calculations to infer relative kinase activities
Usage
KSEA.Complete(KSData, PX, NetworKIN, NetworKIN.cutoff, m.cutoff, p.cutoff)
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 exactly as described below; must have 6 columns in the exact order: Protein, Gene, Peptide, Residue.Both, p, FC; cannot have NA values, or else the entire peptide row is deleted; Description of each column in PX:
|
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 |
Value
creates the following outputs that are deposited into your working directory: a bar plot highlighting key kinase results, a .csv file of all KSEA kinase scores, and a .csv file listing all kinase-substrate relationships used for the calculations
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.Complete(KSData, PX, NetworKIN=TRUE, NetworKIN.cutoff=5, m.cutoff=5, p.cutoff=0.01)
KSEA.Complete(KSData, PX, NetworKIN=FALSE, m.cutoff=2, p.cutoff=0.05)