annotfunc {IMA}R Documentation

Annotate siteIDs/regionIDs of interest

Description

Provide annotation information for a list of site IDs/region IDs of interest

Usage

annotfunc(listtoannot, fullannot, filteredannot, fullIndexannot, 
filteredIndexannot, category = c("site", "region"))

Arguments

listtoannot

a list of site IDs or region IDs of interest

fullannot

the annotation file for all 450k probeIDs

filteredannot

the annotation file for the probeIDs after preprocessing filtering by IMA.methy450PP function

fullIndexannot

Index annotation file containing the full probeIDs/siteIDs for each region, and this object is available as fullannotInd.rda file from http://www.rforge.net/IMA/fullannotInd.rda

filteredIndexannot

Index annotation file containing the probeIDs/siteIDs for each region after preprocessing filtering, and this object is returned by the IMA.methy450PP function

category

category = "site" will indicate site-level annotation, i.e. the "listtoannot" is a list of site-level IDs. Otherwise, the listtoannot is a list of region-level IDs

Value

an annotation matrix for the list of site IDs/region IDs of interest

Author(s)

Dan Wang, Li Yan, Qiang Hu, Dominic J Smiraglia, Song Liu

Maintainer: Dan Wang <wangdan412@gmail.com>

See Also

IMA.methy450R,IMA.methy450PP,regionswrapper,testfunc,sitetest,indexregionfunc,

Examples

###Region level annotation
# >load("./fullannotInd")
# >beta = dataf@bmatrix ##dataf is returned by IMA.methy450PP()
# >betar <- indexregionfunc(indexlist=dataf@TSS1500Ind,beta=beta,indexmethod="mean")
# >TSS1500testALL = testfunc(eset = betar,testmethod="limma",Padj="BH",concov="OFF",
# +groupinfo = dataf2@groupinfo,gcase ="g1",gcontrol="g2",paired = TRUE)
# >TSS1500test = outputDMfunc(TSS1500testALL,rawpcut=0.05,adjustpcut=0.05,betadiffcut=0.14)
# >listtoannot = rownames(TSS1500test)[1:1000]
# >fullIndexannot = TSS1500Ind
# >temp = annotfunc(listtoannot,fullannot,filteredannot,fullIndexannot,
# >filteredIndexannot,category = "region")
  ####site level annotation
# >listtoannot = rownames(sitetest[1:1000,])
# >temp = annotfunc(listtoannot,fullannot,filteredannot,category = "site")

[Package IMA version 3.1.2 Index]