SimBindProfiles (version 1.10.0)

threewayRegions: Classify three Binding Profiles

Description

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

Usage

threewayRegions(xSet, sgrset = c(1, 2, 3), bound.cutoff, diff.cutoff,  probes, probe.max.spacing, writeBedFile=TRUE)

Arguments

xSet

object of class ExpressionSet

sgrset

vector of lenght 3; 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 objects 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 a bed file be written

Value

name

name(s) of data set to which region belongs

class.group

class group; 1 to 7, see details above

chr

chromsome

start

start position of region

end

end position of region

scrore

score of region

nProbes

number of probes in region

Details

Signal values are flagged as bound and unbound, and then the bound probes are classified into 7 groups: class.group=1: unique probes in object 1; class.group=2: unique probes in object 2; class.group=3: unique probes in object 3; class.group=4: common probes in object 1+2; class.group=5: common probes in object 2+3; class.group=6: common probes in object 1+3; class.group=7: common probes in object 1+2+3. The classified probes are then filtered into regions using the probes and probe.max.spacing details. For scores calculations please refer to the pairwiseRegions function. Optional bed file formated result files are written using the choosen options in the file names.

See Also

pairwiseRegions, compensationRegions, increasedBindingRegions

Examples

  dataPath <- system.file("data",package="SimBindProfiles")
  load(file.path(dataPath,"SGR.RData"))
  threewayRegions(SGR, sgrset=c(1,2,3), bound.cutoff=1.86, diff.cutoff=1.4, 
                  probes=10, probe.max.spacing=200)