getSigRegionsCompKC: KCsmart Comparative calculate the signficant regions

Description

Extract the significant regions from a compKC object for a given false discovery rate (FDR).

Usage

getSigRegionsCompKC(compKc, fdr=.01, maxRegionGap=10)

Arguments

compKc

A compKc object as created by the 'compareSpmCollection' function

fdr

The false discovery rate to be used to calculate the significantly different regions from the compKc object

maxRegionGap

The maximum number of sample points that is allowed to fall under the threshold in a continuous significant region

Value

Returns a compKcSigRegions object that contains the significant regions for the given FDR in the 'regionTable' slot. The method used to determine the cutoff, the fdr and the cutoff itself are stored in their corresponding slots. Use 'plot' to visualize the results.

Details

The false discovery rate that is set is used to determine the significant regions. When the compKc object was created by the siggenes method the corresponding cutoff is looked up in the siggenes results table, otherwise it is calculated from the permuted data. The maxRegionGap determines how many sample points can be under this threshold in a continuous significant region.

Examples

Run this code

data(hsSampleData)
data(hsMirrorLocs)

spmc1mb <- calcSpmCollection(hsSampleData, hsMirrorLocs, cl=c(rep(0,10),rep(1,10)))
spmcc1mb <- compareSpmCollection(spmc1mb, nperms=3)
spmcc1mbSigRegions <- getSigRegionsCompKC(spmcc1mb)

plot(spmcc1mb, sigRegions=spmcc1mbSigRegions)