fold.change.filter: Fold change filter

In Anderson-Lab/ComplementaryDomainPrioritization: ComplementaryDomainPrioritization and Filtering

Description

Applies a simple fold change filter on the data.

Usage

fold.change.filter(data, theta, class1.inxs, class2.inxs)

Arguments

data	- transposed gene data
theta	- if > 1, theta is the target number of ranked variables; otherwise, it is the top theta fraction of ranked variables.
class1.inxs	- the row indices of class 1
class2.inxs	- the row indices of class 2

Value

filtered dataset

Examples

download.example.data()
webg.pathways = load.WebGestalt("Marra_0_wiki_protein_enrichment.tsv",'Wiki')
gene.ids = get.genes.wiki(webg.pathways)
Cattaneo.rna = load.gene.data("Cattaneo_array.csv",5)
prioritized.data = list.filter(Cattaneo.rna$transposed.data,gene.ids)
prioritized.filtered.data = fold.change.filter(prioritized.data,100,
                                               which(prioritized.data$labels=='adenoma'),
                                               which(prioritized.data$labels=='normal'))

Anderson-Lab/ComplementaryDomainPrioritization documentation built on May 5, 2019, 5:59 a.m.