Select Ranked Lists

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

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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(DrugVsDisease)
Loading required package: affy
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: biomaRt
Loading required package: ArrayExpress
Loading required package: GEOquery
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: DrugVsDiseasedata
Loading required package: cMap2data

Attaching package: 'cMap2data'

The following object is masked from 'package:DrugVsDiseasedata':

    genelist

Loading required package: qvalue
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DrugVsDisease/selectrankedlists.Rd_%03d_medium.png", width=480, height=480)
> ### Name: selectrankedlists
> ### Title: Select Ranked Lists
> ### Aliases: selectrankedlists
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> data(profiles)
> selectprofile<-selectrankedlists(profiles,1)
> classification<-classifyprofile(data=selectprofile$ranklist,noperm=10,signif.fdr=1)
Number of Significant results greater than 10 Using top 10 hits - consider using average linkage instead
> 
> 
> 
> 
> dev.off()
null device 
          1 
>