ksea: Kinase Set Enrichment Analysis

In evocellnet/ksea: Kinase Activity Prediction based in Quantitative Phosphoproteomic Data

Description

Enrichment of differentially regulated sites in a signature of kinase known targets

Usage

ksea(ranking, norm_express, signature, p = 1, display = TRUE,
  returnRS = FALSE, significance = FALSE, trial = 1000)

Arguments

ranking	Vector of strings containing the ranking of all ids ordered based on their quantifications.
norm_express	Numeric vector with quantifications.
signature	Vector of strings containing all ids in the signature.
p	Numeric value indicating the power at which the weights are scaled.
display	Logical. When TRUE prints the plot of the enrichment.Set to FALSE when running in batch.
returnRS	Logical. If TRUE a list with all the result attributes is returned. If FALSE only a subset is printed based on the value of significance.
significance	Logical. When returnRS is FALSE, if TRUE prints a list with the ES and p-value. If FALSE only the Enrichment Score is printed.
trial	Integer with number of iterations to calculate significance.

Details

The Kinase Set Enrichment Analysis is a established analysis statistical method to look for an enrichment on differentially regulated genes/proteins belonging to a given category in a ranked list usually based on gene expression.

Value

Enrichment result. The output varies depends on the values of returnRS and significance.

Author(s)

David Ochoa (code adapted from Francesco Ioirio's version of the same function).

evocellnet/ksea documentation built on May 16, 2019, 9:40 a.m.