kobas.gage {KOBAS} R Documentation

GAGE style gene set enrichment analysis (KOBAS SNBEA)

Description

<br /> Aggregate the gene level t statistics of each gene set into a gene set level<br /> z-score (sum(t) / sqrt(n)) and estimate the significance from the upper tail<br /> of the standard normal distribution.

Usage

kobas.gage(expr, cls, gmt,
    min.size = 5,
    max.size = 500,
    fdr = "BH",
    data.type = "rseq",
    normalize = TRUE);

Arguments

expr

the expression matrix (matrix object, dataframe or expression matrix file path).

cls

the phenotype class labels, same as the cls parameter of kobas.gsea.

gmt

the gene set collection: a Background model or a GMT file path.

min.size

the minimum number of the mapped members of a gene set, default 5. [as integer]

max.size

the maximum number of the mapped members of a gene set, default 500. [as integer]

fdr

the multiple testing correction method, default BH. [as string]

data.type

the data type of the expression matrix: rseq (default) or ma. [as string]

normalize

performs the data normalization before the analysis? Default TRUE. [as boolean]

env

the R# runtime environment. [as Environment]

Details

The returned p-value is the upper tail probability, that means the gene set is enriched in the second phenotype group (the samples labeled with 1).

Authors

gseakit

Value

a dataframe with the gene set id as the row names and the columns: name, description, size, statistic, pvalue, p_adjust and genes.

clr value class

Examples

[Package KOBAS version 1.0.0.0 Index]