KSEAapp (version 0.99.0)

KSEA.KS_table: The KSEA App Analysis (K-S Dataset Only)

Description

Takes a formatted phoshoproteomics data input and returns just the kinase-subtrate (K-S) annotations used for KSEA calculations

Usage

KSEA.KS_table(KSData, PX, NetworKIN, NetworKIN.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 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)

Value

creates a new data frame in R with all kinase-substrate relationships used for the KSEA 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

KSData.dataset = KSEA.KS_table(KSData, PX, NetworKIN=TRUE, NetworKIN.cutoff=3)
KSData.dataset = KSEA.KS_table(KSData, PX, NetworKIN=FALSE)