threewayRegions: Classify three Binding Profiles

In SimBindProfiles: Similar 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

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.

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

Author(s)

Bettina Fischer, Robert Stojnic

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)

SimBindProfiles documentation built on Nov. 8, 2020, 5:57 p.m.