filteringPaths: Fuction for filtering gene sets with low expression

In GSEMA: Gene Set Enrichment Meta-Analysis

Fuction for filtering gene sets with low expression

Description

This function eliminates gene sets with low expression in both groups in a study

Usage

filteringPaths(objectMApath, threshold = 0.65, n_cores = 1)

Arguments

objectMApath	A list of list. Each list contains two elements. The first element is the Gene Set matrix (gene sets in rows and samples in columns) and the second element is a vector of zeros and ones that represents the state of the different samples of the Gene Sets matrix. 0 represents one group (controls) and 1 represents the other group (cases).
threshold	A number that indicates the threshold to eliminate a gene set. For a eliminate a gene set is necessary that the median for both groups are less than the threshold If threshold = "sd" the threshold will be the standard deviation of the gene set. The default value is 0.65.
n_cores	A number that indicates the number of cores to use in the parallelization. The default value is 1.

Value

The same objectMApath list but with the gene sets that do not meet the threshold eliminated.

Author(s)

Juan Antonio Villatoro Garcia, [e-mail]

See Also

createObjectMApath

Examples

data("simulatedData")
newObject <- filteringPaths(objectMApathSim, threshold = "sd")

GSEMA documentation built on Oct. 14, 2024, 5:09 p.m.