selectrankedlists: Select Ranked Lists

In clarepacini/DrugVsDisease: Comparison of disease and drug profiles using Gene set Enrichment Analysis

Description

Given a list with two elements, one containing ranklists for a set of regression models and the second containing the associated p-values. This function is used to extract a subset of the models.

Usage

selectrankedlists(ranklist, colsinc)

Arguments

ranklist	List with two elements (as output from generate profiles): Ranklist: Matrix containing the ranks of gene expression. Rows containing the genes, columns the different profiles. Pvalues: Matrix containing the associated p-values to the differential expression profiles in Ranklist.
colsinc	Vector of integers containing the column references of the profiles to select.

Details

Format of list provided to selectrankedlists is the same as is output from generateprofiles generateprofiles. The output from selectrankedlists can be used as input to the classify profile function classifyprofile.

Value

Ranklist	Matrix containing the ranks of gene expression. Rows containing the genes, columns the selected profiles
Pvalues	Matrix containing the associated p-values to the differential expression profiles in Ranklist

Author(s)

C. Pacini

Source

http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-22528

See Also

generateprofiles, classifyprofile.

Examples

data(profiles)
selectprofile<-selectrankedlists(profiles,1)
classification<-classifyprofile(data=selectprofile$ranklist,noperm=10,signif.fdr=1)

clarepacini/DrugVsDisease documentation built on May 24, 2019, 7:21 p.m.