make filter of the background model

geneSet.filter {background}

R Documentation

make filter of the background model

Description

Usage

geneSet.filter(background, geneSet,
    min.size = 3,
    max.intersects = 500);

Arguments

background

[as Background]

geneSet

usually be a character of the gene id set.

min.size

the min feature size is required for each cluster. all of the cluster that have the feature number less than this cutoff will be removed from the background. [as integer]

max.intersects

the max intersect number that each cluster intersect with the input geneSet. all of the clusters that greater than this value will be removed from the background. [as integer]

Authors

gseakit

Value

a new background model that has cluster filtered by the given rule.

clr value class

Background

Examples

 let kb = read.background("hsa.xml");
 let idset = c("id1","id2","id3");
 let filter_kb = kb |> geneSet.filter(idset, min.size=5, max.intersects=500);
 
 print(background_summary(filter_kb));

[Package background version 1.0.0.0 Index]