SimBindProfiles (version 1.10.0)

pairwiseRegions: Classify two Binding Profiles

Description

Classify two Binding Profiles into unique and common binding regions and write results to bed files.

Usage

pairwiseRegions(xSet, sgrset = c(1, 2), bound.cutoff, diff.cutoff, probes, probe.max.spacing, writeBedFile=TRUE)

Arguments

xSet

object of class ExpressionSet

sgrset

vector of lenght 2; specifying which data sets to compare from the ExpressionSet

bound.cutoff

numeric; threshold above probes are considered “bound”

diff.cutoff

numeric; difference threshold to determine if object 1 and object 2 are unqiquely bound

probes

integer; minimum number of probes in a valid region

probe.max.spacing

integer; maximum number of base pairs in a gap before splitting a region into 2 regions

writeBedFile

logical; should bed file be written

Value

data.frame with the following columns:

name

name(s) of data set to which region belongs

class.group

class group; 1, 2 or 3 for common regions between both sets

chr

chromsome

start

start position of region

end

end position of region

scrore

score of region

nProbes

number of probes in region

Details

Probe signal values above the bound.cutoff in both data are classified as common bound. Probes which are above the bound.cutoff and in one data and higher than the diff.cutoff to the other data are called unique. Then these probes are then filtered into regions using the probes and probe.max.spacing details. The score for the unique regions is calculated as mean (probes in region set 1 minus set 2), or vise versa. The score for the common region is the mean (probes in region (set 1 plus set 2)/2). Optional bed file formated result files are written using the choosen options in the file names.

See Also

compensationRegions, increasedBindingRegions, threewayRegions

Examples

  dataPath <- system.file("data",package="SimBindProfiles")
  load(file.path(dataPath,"SGR.RData"))
  pairAB <- pairwiseRegions(SGR, sgrset=c(1,2), bound.cutoff=1.86, diff.cutoff=1.4, 
            probes=10, probe.max.spacing=200)