KSEAapp (version 0.99.0)

KSEA.Complete: 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:

• "Protein" the Uniprot ID for the parent protein
• "Gene" the HUGO gene name for the parent protein
• "Peptide" the peptide sequence
• "Residue.Both" all phosphosites from that peptide, separated by semicolons if applicable; must be formatted as the single amino acid abbrev. with the residue position (e.g. S102)
• "p" the p-value of that peptide (if none calculated, please write "NULL", cannot be NA)
• "FC" the fold change (not log-transformed); usually the control sample is the denominator

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)